Stopping on breakpoint can cause X window system to freeze
I was experiencing this problem when debugging a Java Swing app on my Ubuntu system. When by debugger hit a breakpoint, sometimes the whole X window system would freeze. My only option was to drop to the console (ctrl-alt-f1) and kill the java process. This fix seems to have fixed it:
Add the java VM options:
-Dsun.awt.disablegrab=true
for more details see this