Thanks for suggestion.
I had problem with keyboard and Swing/AWT apps in Ubuntu and read lot of X related info on the internet which pointed problems to SCIM. However this issue was due to lost environment variable "AWT_TOOLIK=MToolkit" (should be XToolkit, is by default) set in /etc/environment (set when first trying Compiz to fix some Java rendering issues).
I already solved the issue with IDEA when I find out that I can't use Ctrl-F[1-12] shortcuts even in Eclipse. They were set to switch to virtual desktops by default
. I'll search deeper next time.