Please use the following simple test program to reproduce:

import java.awt.GraphicsEnvironment;
import java.awt.GraphicsDevice;
import java.awt.DisplayMode;

public class Test {

     public static void main(String[] args) {

         GraphicsEnvironment env = GraphicsEnvironment.getLocalGraphicsEnvironment();

         GraphicsDevice devices[] = env.getScreenDevices();
         for (int d = 0; d < devices.length; ++d) {
             GraphicsDevice dev = devices[d];
             System.out.println("Device: " + dev.toString());
             DisplayMode modes[] = dev.getDisplayModes();
             System.out.println("Resolutions:");
             for (int m = 0; m < modes.length; ++m) {
                 System.out.println(modes[m].getHeight() + "x" + modes[m].getWidth());
             }
         }
     }
}


Compile and run it on a system with two displays. Here is output when both display are switched on (note: only current resolutions are listed):
Device: X11GraphicsDevice[screen=0]
Resolutions:
966x1280
Device: X11GraphicsDevice[screen=1]
Resolutions:
920x1280

Here is a responding xrandr output:
Screen 0: minimum 64 x 64, current 2560 x 966, maximum 32000 x 32000
VBOX0 connected 1280x966+0+0 0mm x 0mm
   1280x966 60.0*+
   1280x960 60.0
   1024x768 60.0
   800x600 60.0
   640x480 60.0
VBOX1 connected 1280x920+1280+0 0mm x 0mm
   1280x920 60.0*+
   1280x960 60.0
   1024x768 60.0
   800x600 60.0
   640x480 60.0

Then try to switch one of the displays (e.g., System Settings->Displays etc.) off and run the test again. The test output looks like:
Device: X11GraphicsDevice[screen=0]
Resolutions:
966x1280
960x1280
768x1024
600x800
480x640

JDK used: 8 b101
OS version: Ubuntu 12.04; VirtualBox was used, but on my colleague's non-virtual machine (Ubuntu) the issue is reproducible too.

On Windows this test works as expected (two full resolution lists obtained).