Product Version = NetBeans IDE 8.2 (Build 201609300101)
Operating System = Windows 7 version 6.1 running on amd64
Java; VM; Vendor = 1.8.0_111
Runtime = Java HotSpot(TM) 64-Bit Server VM 25.111-b14

Reproducibility: Happens every time

The error is repeatable.

STEPS:
  * Create two Java files with similar names (PopUpColorMenu & PopUpColorMenu2)
  * Click on PopUpColorMenu
  * Set breakpoint
  * Click on PopUpColorMenu2
  * Click on Debug File
  * Break at breakpoint set in PopUpColorMenu 

ACTUAL:
  PopUpColorMenu executes

EXPECTED:
 PopUpColorMenu2 executes


I don't see a tab to contain the code (abou 140 lines), so!!!

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package snark;

//file: PopUpColorMenu.java
import java.awt.*;
import java.awt.event.*;
import javax.swing.*;

public class PopUpColorMenu implements ActionListener {
   Component selectedComponent;

   public PopUpColorMenu() {
      JFrame frame = new JFrame("PopUpColorMenu v1.0");
      frame.setLocation(200, 100);
      frame.setSize(200,70);

      final JPopupMenu colorMenu = new JPopupMenu("Color");
      colorMenu.add(makeMenuItem("Red"));
      colorMenu.add(makeMenuItem("Green"));
      colorMenu.add(makeMenuItem("Blue"));

      MouseListener mouseListener = new MouseAdapter() {
         public void mousePressed(MouseEvent e) { checkPopup(e); }
         public void mouseClicked(MouseEvent e) { checkPopup(e); }
         public void mouseReleased(MouseEvent e) { checkPopup(e); }
         private void checkPopup(MouseEvent e) {
            if (e.isPopupTrigger()) {
               selectedComponent = e.getComponent();
               colorMenu.show(e.getComponent(), e.getX(), e.getY());
            }
           }
      };

      Container content = frame.getContentPane(); // unnecessary  in 5.0+
      content.setLayout(new FlowLayout());
      JButton button = new JButton("Uno");
      button.addMouseListener(mouseListener);
      content.add(button);
      
      button = new JButton("Due");
      button.addMouseListener(mouseListener);
      content.add(button);
      
      button = new JButton("Tre");
      button.addMouseListener(mouseListener);
      content.add(button);

      frame.getContentPane().addMouseListener(mouseListener);

      frame.setDefaultCloseOperation( JFrame.EXIT_ON_CLOSE );
      frame.setVisible(true);
   }

   public void actionPerformed(ActionEvent e) {
      String color = e.getActionCommand();
      if (color.equals("Red"))
        selectedComponent.setBackground(Color.red);
      else if (color.equals("Green"))
        selectedComponent.setBackground(Color.green);
      else if (color.equals("Blue"))
        selectedComponent.setBackground(Color.blue);
   }

   private JMenuItem makeMenuItem(String label) {
      JMenuItem item = new JMenuItem(label);
      item.addActionListener( this );
      return item;
   }

   public static void main(String[] args) {
      new PopUpColorMenu();
   }
}
-----------------------------------------------------------------------------------------------

package snark;

//file: PopUpColorMenu.java
import java.awt.*;
import java.awt.event.*;
import javax.swing.*;

public class PopUpColorMenu2 implements ActionListener {
   Component selectedComponent;
   
   public PopUpColorMenu2() {
      String[] colors = { "uno", "due", "tre" };
      JButton button;
      
      JFrame frame = new JFrame("PopUpColorMenu v1.0");
      frame.setLocation(200, 100);
      frame.setSize(200,70);

      final JPopupMenu colorMenu = new JPopupMenu("Color");
      colorMenu.add(makeMenuItem("Red"));
      colorMenu.add(makeMenuItem("Green"));
      colorMenu.add(makeMenuItem("Orange"));

      MouseListener mouseListener = new MouseAdapter() {
         public void mousePressed(MouseEvent e) { checkPopup(e); }
         public void mouseClicked(MouseEvent e) { checkPopup(e); }
         public void mouseReleased(MouseEvent e) { checkPopup(e); }
         private void checkPopup(MouseEvent e) {
            if (e.isPopupTrigger()) {
               selectedComponent = e.getComponent();
               colorMenu.show(e.getComponent(), e.getX(), e.getY());
            }
           }
      };

      Container content = frame.getContentPane(); // unnecessary  in 5.0+
      content.setLayout(new FlowLayout());
      
      for (String str : colors) { 
          button = new JButton(str);
          content.add(button);
          button.addMouseListener(mouseListener);
      }

      frame.getContentPane().addMouseListener(mouseListener);

      frame.setDefaultCloseOperation( JFrame.EXIT_ON_CLOSE );
      frame.setVisible(true);
   }

   public void actionPerformed(ActionEvent e) {
      String color = e.getActionCommand();
      if (color.equals("Red"))
        selectedComponent.setBackground(Color.red);
      else if (color.equals("Green"))
        selectedComponent.setBackground(Color.green);
      else if (color.equals("Orange"))
        selectedComponent.setBackground(Color.ORANGE);
   }

   private JMenuItem makeMenuItem(String label) {
      JMenuItem item = new JMenuItem(label);
      item.addActionListener( this );
      return item;
   }

   public static void main(String[] args) {
      new PopUpColorMenu();
   }
}