Breakpoint sometimes blocks complete desktop

If I put a breakpoint in IntelliJ (8.1.3) while debugging a Java app, and the breakpoint breaks at the moment when in the debugged app I was opening a combobox or a popup menu, then sometimes my complete desktop blocks. I mean everything blocks. Nothing responds to the mouse anymore. IntelliJ doesn't, the taskbar doesn't, any other open program doesn't.

This in Ubuntu.

The only way out is to press "ctrl+alt+F6", login to the text mode screen, do "ps -eal | grep java", and "kill -9" with the id of the most recent java process in the resulting list. Then I can go back to my desktop and work again.

But this is very annoying.

Why does the whole system hang with IntelliJ's breakpoints and how can I avoid this?