A DESCRIPTION OF THE PROBLEM :
Prior to Java 8 Update 131 pressing Command + ~ on the Mac would cycle through all JFrames created by a Java application.  This was consistent with the behavior of native Apps.  As of this update, pressing Command + ~ merely switches back and forth between a pair of JFrames.

This most likely related to the following note in the Java Update 131 Release Highlights:

Bug Fix: Introduce new window ordering model ...


STEPS TO FOLLOW TO REPRODUCE THE PROBLEM :
1. Run the test case.  It will open three JFrames
2. Press Command + ~ repeatedly

EXPECTED VERSUS ACTUAL BEHAVIOR :
EXPECTED -
Expect Command + ~ to cycle through the three JFrames
ACTUAL -
Instead it merely switches back and forth between two of them.

---------- BEGIN SOURCE ----------
import javax.swing.*;

public class JavaFrames {

    public static void main(String s[]) {
        JFrame windowA = new JFrame("Window A");
        windowA.setLocation(20, 20);
        windowA.setSize(300, 100);
        windowA.setVisible(true);
        
        JFrame windowB = new JFrame("Window B");
        windowB.setLocation(40, 70);
        windowB.setSize(300, 100);
        windowB.setVisible(true);
        
        JFrame windowC = new JFrame("Window C");
        windowC.setLocation(60, 120);
        windowC.setSize(300, 100);
        windowC.setVisible(true);
    }
}

---------- END SOURCE ----------

CUSTOMER SUBMITTED WORKAROUND :
Command + Shift + ~ still cycles through all application JFrames but in reverse order.

FREQUENCY : always