Hay dos problemas: uno en la clase AutoCompletar y otro en Prueba.

1.- Elimina todas las referencias static en AutoCompletar. Es lo que causa que solo funcione una única instancia de AutoCompletar.

2.- Usa diferentes variables para las instancias de AutoCompletar en Prueba. Tal y como lo tienes, usas la misma para ambos JTextField.

Al margen de esto, procura seguir las convenciones sintácticas de Java: las variables empiezan con letra minúscula.

Siguen nuevas versiones mejoradas de ambas clases.

import java.util.ArrayList;
import javax.swing.DefaultComboBoxModel;

public class Prueba extends javax.swing.JFrame {

private AutoCompletar autoMarcas, autoProductos;
private final DefaultComboBoxModel modeloComboMarca;
private final DefaultComboBoxModel modeloComboProductos;
private ArrayList<String> itemsMarca;
private ArrayList<String> itemsTipoProducto;

/**
Creates new formodeloComboProductos Prueba
*/
public Prueba() {
this.modeloComboMarca = new DefaultComboBoxModel();
this.modeloComboProductos = new DefaultComboBoxModel();
this.itemsTipoProducto = new ArrayList<>();
this.itemsMarca = new ArrayList<>();
initComponents();
AutocompleatadoMarca();
AutocompleatadoTipoProducto();

}

private void AutocompleatadoMarca() {

autoMarcas = new AutoCompletar(modeloComboMarca, jtxtMarca);

itemsMarca.clear();

itemsMarca.add("MERCEDES");
itemsMarca.add("TOYOTA");
itemsMarca.add("KIA");
itemsMarca.add("MAZDA3");
itemsMarca.add("HONDA");

autoMarcas.setupAutoComplete(itemsMarca);

}

private void AutocompleatadoTipoProducto() {

autoProductos = new AutoCompletar(modeloComboProductos, jtxtTipoProducto);

itemsTipoProducto.clear();

itemsTipoProducto.add("AUTOMOVIL");
itemsTipoProducto.add("MOTO LINEAL");
itemsTipoProducto.add("CAMION");
itemsTipoProducto.add("CAMIONETA");

autoProductos.setupAutoComplete(itemsTipoProducto);

}

/**
This modeloComboProductosethod is called fromodeloComboProductos within the constructor to initialize the formodeloComboProductos.
WARNING: Do NOT modeloComboProductosodify this code. The content of this modeloComboProductosethod is always
regenerated by the FormodeloComboProductos Editor.
*/
@SuppressWarnings("unchecked")
// <editor-fold defaultstate="collapsed" desc="Generated Code">
private void initComponents() {

jtxtMarca = new javax.swing.JTextField();
jtxtTipoProducto = new javax.swing.JTextField();

setDefaultCloseOperation(javax.swing.WindowConstants.EXIT_ON_CLOSE);

javax.swing.GroupLayout layout = new javax.swing.GroupLayout(getContentPane());
getContentPane().setLayout(layout);
layout.setHorizontalGroup(
layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGroup(layout.createSequentialGroup()
.addGap(20, 20, 20)
.addComponent(jtxtMarca, javax.swing.GroupLayout.PREFERRED_SIZE, 155, javax.swing.GroupLayout.PREFERRED_SIZE)
.addGap(38, 38, 38)
.addComponent(jtxtTipoProducto, javax.swing.GroupLayout.PREFERRED_SIZE, 162, javax.swing.GroupLayout.PREFERRED_SIZE)
.addContainerGap(25, Short.MAX_VALUE))
);
layout.setVerticalGroup(
layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGroup(layout.createSequentialGroup()
.addGap(91, 91, 91)
.addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
.addComponent(jtxtMarca, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
.addComponent(jtxtTipoProducto, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
.addContainerGap(189, Short.MAX_VALUE))
);

pack();
}// </editor-fold>

/**
@param args the comodeloComboProductosmodeloComboProductosand line argumodeloComboProductosents
*/
public static void main(String args[]) {
/* Set the Nimbus look and feel */
//<editor-fold defaultstate="collapsed" desc=" Look and feel setting code (optional) ">
/* If Nimbus (introduced in Java SE 6) is not available, stay with the default look and feel.
* For details see http://download.oracle.com/javase/tutorial/uiswing/lookandfeel/plaf.html
*/
try {
for (javax.swing.UIManager.LookAndFeelInfo info : javax.swing.UIManager.getInstalledLookAndFeels()) {
if ("Nimbus".equals(info.getName())) {
javax.swing.UIManager.setLookAndFeel(info.getClassName());
break;
}
}
} catch (ClassNotFoundException ex) {
java.util.logging.Logger.getLogger(Prueba.class.getName()).log(java.util.logging.Level.SEVERE, null, ex);
} catch (InstantiationException ex) {
java.util.logging.Logger.getLogger(Prueba.class.getName()).log(java.util.logging.Level.SEVERE, null, ex);
} catch (IllegalAccessException ex) {
java.util.logging.Logger.getLogger(Prueba.class.getName()).log(java.util.logging.Level.SEVERE, null, ex);
} catch (javax.swing.UnsupportedLookAndFeelException ex) {
java.util.logging.Logger.getLogger(Prueba.class.getName()).log(java.util.logging.Level.SEVERE, null, ex);
}
//</editor-fold>

/* Create and display the form */
java.awt.EventQueue.invokeLater(new Runnable() {
public void run() {
new Prueba().setVisible(true);
}
});
}

// Variables declaration - do not modify
private javax.swing.JTextField jtxtMarca;
private javax.swing.JTextField jtxtTipoProducto;
// End of variables declaration
}

import java.awt.BorderLayout;
import java.awt.Dimension;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.awt.event.KeyAdapter;
import java.awt.event.KeyEvent;
import java.util.ArrayList;
import javax.swing.ComboBoxModel;
import javax.swing.DefaultComboBoxModel;
import javax.swing.JComboBox;
import javax.swing.JTextField;
import javax.swing.event.DocumentEvent;
import javax.swing.event.DocumentListener;

/**
<p>
@author Carlos
*/
public class AutoCompletar {

private final DefaultComboBoxModel modelo;
private KeyAdapter keyAdapter;
private final JTextField txtInput;
private JComboBox cbInput;

/**
<p>
@param modelo
@param txtInputt
*/
public AutoCompletar(DefaultComboBoxModel modelo, JTextField txtInputt) {
this.modelo = modelo;
this.txtInput = txtInputt;
}

/**
<p>
*/
public void ElimacionKeyListener() {
txtInput.removeKeyListener(keyAdapter);
}

/**
<p>
@param items
*/
public void setupAutoComplete(final ArrayList<String> items) {

cbInput = new JComboBoxImpl(modelo);
modelo.removeAllElements();

setAdjusting(false);
for (String item : items) {
modelo.addElement(item);
}
cbInput.setSelectedItem(null);
cbInput.addActionListener(new ActionListenerImpl());

keyAdapter = new KeyAdapterImpl();
txtInput.addKeyListener(keyAdapter);
txtInput.getDocument().addDocumentListener(new DocumentListenerImpl(items));
txtInput.setLayout(new BorderLayout());
txtInput.add(cbInput, BorderLayout.SOUTH);
}

private void setAdjusting(boolean adjusting) {
cbInput.putClientProperty("is_adjusting", adjusting);
}

private class DocumentListenerImpl implements DocumentListener {

private final ArrayList<String> items;

DocumentListenerImpl(ArrayList<String> items) {
this.items = items;
}

@Override
public void insertUpdate(DocumentEvent e) {
updateList();
}

@Override
public void removeUpdate(DocumentEvent e) {
updateList();
}

@Override
public void changedUpdate(DocumentEvent e) {
updateList();
}

private void updateList() {
setAdjusting(true);
modelo.removeAllElements();
String input = txtInput.getText();
if (!input.isEmpty() || input.isEmpty()) {
for (String item : items) {
if (item.toLowerCase().contains(input.toLowerCase())) {
modelo.addElement(item);
cbInput.setPopupVisible(modelo.getSize() < 0);
}
}
}
if (!input.isEmpty()) {
cbInput.setPopupVisible(modelo.getSize() > 0);
setAdjusting(false);
}
}
}

private class KeyAdapterImpl extends KeyAdapter {

@Override
public void keyPressed(KeyEvent e) {
setAdjusting(true);
if (e.getKeyCode() == KeyEvent.VK_DOWN || e.getKeyCode() == KeyEvent.VK_UP) {
cbInput.setPopupVisible(true);
}
if (cbInput.isPopupVisible()) {
if (e.getKeyCode() == KeyEvent.VK_ENTER || e.getKeyCode() == KeyEvent.VK_UP || e.getKeyCode() == KeyEvent.VK_DOWN) {
e.setSource(cbInput);
cbInput.dispatchEvent(e);
if (e.getKeyCode() == KeyEvent.VK_ENTER) {
txtInput.setText(cbInput.getSelectedItem().toString());
cbInput.setPopupVisible(false);
}
}
}
if (e.getKeyCode() == KeyEvent.VK_ESCAPE) {
cbInput.setPopupVisible(false);
}
setAdjusting(false);
}
}

private class ActionListenerImpl implements ActionListener {

@Override
public void actionPerformed(ActionEvent e) {
if (!isAdjusting()) {
if (cbInput.getSelectedItem() != null) {
txtInput.setText(cbInput.getSelectedItem().toString());
}
}
}

private boolean isAdjusting() {
if (cbInput.getClientProperty("is_adjusting") instanceof Boolean) {
return (Boolean) cbInput.getClientProperty("is_adjusting");
}
return false;
}
}

private class JComboBoxImpl extends JComboBox {

JComboBoxImpl(ComboBoxModel aModel) {
super(aModel);
}

@Override
public Dimension getPreferredSize() {
return new Dimension(super.getPreferredSize().width, 0);
}
}
}

Voy a mirarlo con detenimiento, porque esa clase AutoCompletar es un poco "frankestein" :)
Es inevitable hacerle bastantes modificaciones. Mañana te digo algo.

"frankestein": hecho con trozos, feo y da miedo :)

import java.awt.BorderLayout;
import java.awt.Dimension;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.awt.event.KeyAdapter;
import java.awt.event.KeyEvent;
import java.util.ArrayList;
import java.util.List;
import java.util.Locale;
import javax.swing.ComboBoxModel;
import javax.swing.DefaultComboBoxModel;
import javax.swing.JComboBox;
import javax.swing.JTextField;
import javax.swing.event.DocumentEvent;
import javax.swing.event.DocumentListener;

/**
<p>
@author Carlos
*/
public class AutoCompletar2 {

private final DefaultComboBoxModel<String> modelo;
private final JTextField txtInput;
private final JComboBox<String> cbInput;
private final DocumentListenerImpl documentListener;

/**
<p>
@param txtInputt
*/
public AutoCompletar2(JTextField txtInputt) {
this.txtInput = txtInputt;

modelo = new DefaultComboBoxModel<>();
cbInput = new JComboBoxImpl(modelo);
cbInput.setSelectedItem(null);
cbInput.addActionListener(new ActionListenerImpl());

txtInput.addKeyListener(new KeyAdapterImpl());
documentListener = new DocumentListenerImpl();
txtInput.getDocument().addDocumentListener(documentListener);
txtInput.setLayout(new BorderLayout());
txtInput.add(cbInput, BorderLayout.SOUTH);
}

/**
<p>
@param items
*/
public void setupAutoComplete(final List<String> items) {
documentListener.añadirItems(items);
modelo.removeAllElements();
setAdjusting(false);
for (String item : items) {
modelo.addElement(item);
}
cbInput.setSelectedItem(null);
txtInput.setText(null);
}

private void setAdjusting(boolean adjusting) {
cbInput.putClientProperty("is_adjusting", adjusting);
}

private static class JComboBoxImpl extends JComboBox<String> {

private static final long serialVersionUID = -1758572388906268539L;

JComboBoxImpl(ComboBoxModel<String> aModel) {
super(aModel);
}

@Override
public Dimension getPreferredSize() {
return new Dimension(super.getPreferredSize().width, 0);
}
}

private class DocumentListenerImpl implements DocumentListener {

private List<String> items;

private void añadirItems(final List<String> items) {
this.items = new ArrayList<>(items);
}

@Override
public void insertUpdate(DocumentEvent e) {
updateList();
}

@Override
public void removeUpdate(DocumentEvent e) {
updateList();
}

@Override
public void changedUpdate(DocumentEvent e) {
updateList();
}

private void updateList() {
setAdjusting(true);
modelo.removeAllElements();
String input = txtInput.getText();
boolean empty = input.isEmpty();
if (!empty || empty) {
Locale locale = Locale.getDefault();
for (String item : items) {
if (item.toLowerCase(locale).contains(input.toLowerCase(locale))) {
modelo.addElement(item);
cbInput.setPopupVisible(modelo.getSize() < 0);
}
}
}
if (!empty) {
cbInput.setPopupVisible(modelo.getSize() > 0);
setAdjusting(false);
}
}
}

private class KeyAdapterImpl extends KeyAdapter {

@Override
public void keyPressed(KeyEvent e) {
setAdjusting(true);
int code = e.getKeyCode();
if (code == KeyEvent.VK_DOWN || code == KeyEvent.VK_UP) {
cbInput.setPopupVisible(true);
}
if (cbInput.isPopupVisible()) {
if (code == KeyEvent.VK_ENTER || code == KeyEvent.VK_UP || code == KeyEvent.VK_DOWN) {
e.setSource(cbInput);
cbInput.dispatchEvent(e);
if (code == KeyEvent.VK_ENTER) {
txtInput.setText(cbInput.getSelectedItem().toString());
cbInput.setPopupVisible(false);
}
}
}
if (code == KeyEvent.VK_ESCAPE) {
cbInput.setPopupVisible(false);
}
setAdjusting(false);
}
}

private class ActionListenerImpl implements ActionListener {

@Override
public void actionPerformed(ActionEvent e) {
if (!isAdjusting()) {
if (cbInput.getSelectedItem() != null) {
txtInput.setText(cbInput.getSelectedItem().toString());
}
}
}

private boolean isAdjusting() {
return cbInput.getClientProperty("is_adjusting") instanceof Boolean ? (Boolean) cbInput.getClientProperty("is_adjusting") : false;
}
}
}

import java.util.ArrayList;

public class Prueba extends javax.swing.JFrame {

private static final long serialVersionUID = 7510262562109501827L;

/**
@param args the command line arguments
*/
public static void main(String args[]) {
/* Set the Nimbus look and feel */
//<editor-fold defaultstate="collapsed" desc=" Look and feel setting code (optional) ">
/* If Nimbus (introduced in Java SE 6) is not available, stay with the default look and feel.
* For details see http://download.oracle.com/javase/tutorial/uiswing/lookandfeel/plaf.html
*/
try {
for (javax.swing.UIManager.LookAndFeelInfo info : javax.swing.UIManager.getInstalledLookAndFeels()) {
if ("Nimbus".equals(info.getName())) {
javax.swing.UIManager.setLookAndFeel(info.getClassName());
break;
}
}
} catch (ClassNotFoundException ex) {
java.util.logging.Logger.getLogger(Prueba.class.getName()).log(java.util.logging.Level.SEVERE, null, ex);
} catch (InstantiationException ex) {
java.util.logging.Logger.getLogger(Prueba.class.getName()).log(java.util.logging.Level.SEVERE, null, ex);
} catch (IllegalAccessException ex) {
java.util.logging.Logger.getLogger(Prueba.class.getName()).log(java.util.logging.Level.SEVERE, null, ex);
} catch (javax.swing.UnsupportedLookAndFeelException ex) {
java.util.logging.Logger.getLogger(Prueba.class.getName()).log(java.util.logging.Level.SEVERE, null, ex);
}
//</editor-fold>

/* Create and display the form */
java.awt.EventQueue.invokeLater(new Runnable() {
@Override
public void run() {
new Prueba().setVisible(true);
}
});
}

private final AutoCompletar2 autoMarcas, autoProductos;
private final ArrayList<String> itemsMarca;
private final ArrayList<String> itemsTipoProducto;

// Variables declaration - do not modify
private javax.swing.JButton jbtnCancelar;
private javax.swing.JButton jbtnNuevo;
private javax.swing.JTextField jtxtMarca;
private javax.swing.JTextField jtxtTipoProducto;
// End of variables declaration

/**
Creates new form Prueba
*/
public Prueba() {

this.itemsTipoProducto = new ArrayList<>();
this.itemsMarca = new ArrayList<>();
initComponents();

this.jtxtMarca.setText(null);
this.jtxtTipoProducto.setText(null);
this.jtxtMarca.setEnabled(false);
this.jtxtTipoProducto.setEnabled(false);

autoMarcas = new AutoCompletar2(jtxtMarca);
autoProductos = new AutoCompletar2(jtxtTipoProducto);

}

private void autocompletadoMarca() {

itemsMarca.clear();

itemsMarca.add("MERCEDES");
itemsMarca.add("TOYOTA");
itemsMarca.add("KIA");
itemsMarca.add("MAZDA3");
itemsMarca.add("HONDA");

autoMarcas.setupAutoComplete(itemsMarca);

}

private void autocompletadoTipoProducto() {

itemsTipoProducto.clear();

itemsTipoProducto.add("AUTOMOVIL");
itemsTipoProducto.add("MOTO LINEAL");
itemsTipoProducto.add("CAMION");
itemsTipoProducto.add("CAMIONETA");

autoProductos.setupAutoComplete(itemsTipoProducto);

}

/**
This method is called from within the constructor to initialize the form.
WARNING: Do NOT modify this code. The content of this method is always
regenerated by the Form Editor.
*/
@SuppressWarnings("unchecked")
// <editor-fold defaultstate="collapsed" desc="Generated Code">
private void initComponents() {

jtxtMarca = new javax.swing.JTextField();
jtxtTipoProducto = new javax.swing.JTextField();
jbtnNuevo = new javax.swing.JButton();
jbtnCancelar = new javax.swing.JButton();

setDefaultCloseOperation(javax.swing.WindowConstants.EXIT_ON_CLOSE);

jbtnNuevo.setText("NUEVO");
jbtnNuevo.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
jbtnNuevoActionPerformed(evt);
}
});

jbtnCancelar.setText("CANCELAR");
jbtnCancelar.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
jbtnCancelarActionPerformed(evt);
}
});

javax.swing.GroupLayout layout = new javax.swing.GroupLayout(getContentPane());
getContentPane().setLayout(layout);
layout.setHorizontalGroup(
layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGroup(layout.createSequentialGroup()
.addGap(23, 23, 23)
.addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING, false)
.addComponent(jtxtMarca)
.addComponent(jbtnCancelar, javax.swing.GroupLayout.DEFAULT_SIZE, 159, Short.MAX_VALUE))
.addGap(18, 18, 18)
.addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING, false)
.addComponent(jbtnNuevo, javax.swing.GroupLayout.DEFAULT_SIZE, 164, Short.MAX_VALUE)
.addComponent(jtxtTipoProducto))
.addContainerGap(36, Short.MAX_VALUE))
);
layout.setVerticalGroup(
layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGroup(layout.createSequentialGroup()
.addGap(91, 91, 91)
.addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
.addComponent(jtxtMarca, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
.addComponent(jtxtTipoProducto, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
.addGap(42, 42, 42)
.addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
.addComponent(jbtnNuevo)
.addComponent(jbtnCancelar))
.addContainerGap(124, Short.MAX_VALUE))
);

pack();
}// </editor-fold>

private void jbtnNuevoActionPerformed(java.awt.event.ActionEvent evt) {

this.jtxtMarca.setText(null);
this.jtxtTipoProducto.setText(null);
this.jtxtMarca.setEnabled(true);
this.jtxtTipoProducto.setEnabled(true);

autocompletadoMarca();
autocompletadoTipoProducto();

}

private void jbtnCancelarActionPerformed(java.awt.event.ActionEvent evt) {
this.jtxtMarca.setText(null);
this.jtxtTipoProducto.setText(null);
this.jtxtMarca.setEnabled(false);
this.jtxtTipoProducto.setEnabled(false);
}
}

No sé que haya un evento del tipo que mencionas: agregar o eliminar una fila.
Lo que si existe es un TableModelListener, por ejemplo:

jTable1.getModel().addTableModelListener(new TableModelListener() {
public void tableChanged(TableModelEvent e) {
if(e.getType() == e.UPDATE){
// la tabla se ha modificado
}
}
});

que permite saber qué tipo de evento se ha disparado con un cambio en la tabla.

http://docs.oracle.com/javase/7/docs/api/javax/swing/event/TableModelEvent.html#getType()

Dentro de ese método puedes comprobar el tamaño del modelo de la tabla, para saber si hay filas o no.