The problem still persists, even with java version 1.7.0_25. I've attached the full stdout and stderr. Sometimes the window will become responsive again after about 10 or 20 seconds, but sometimes (like in the attached file) I have to just kill the process. All of the IOExceptions at the end came after killing the process.
Resolved, new version (1.7.0_25) fixed it. Thanks.
"clicked-close.png" shows after I clicked close, when the window can still be seen in the taskbar above but is no longer on the screen and I can't switch to it. "reappeared.png" is after I switched to a different desktop and back. The window is completely frozen and can't be closed or interacted with.
I also attached an exception that was thrown when I tried to click on an element in the frozen window shown in "reappeared.png".
I just tried with 1.6.1, and it's still happening.