Ever since I upgraded to Ubuntu 14.04 I have been running into what looks like a glass GTK bug that affects our robot-based system tests. The symptom is that the window position of a secondary, decorated stage is not properly reflected in the stage X and Y properties. On my system it is usually Y that is wrong.

I was able to narrow it down using the following test program. To reproduce it, run the attached program (you may need to run it more than once) as follows:

1. Run the program
2. Wait (without touching the mouse) until the label changes from "Waiting..." to "Cursor should now be centered on red circle"
3. BUG: sometimes the cursor will be offset by a few pixels -- typically 10 pixels below on my system

You can run "xwininfo" and compare the output to the "Inner" values. They are supposed to match, but will not when the bug reproduces.

If you then click the "Reposition" button and wait again (without touching the mouse), it will try again, and fail again. Clicking outside (to lose focus) and back in (to regain focus) the JavaFX stage is sufficient to fix the problem.

I can also reproduce this by maximizing the window using the UI shortcut of dragging the window to the top of the screen, and then unmaximizing it with the window "Restore" button (which is in the top toolbar for a maximized window).

I suspect that this might be related to other async issues on Linux, but cannot be sure.