PyCharm is not responding on Ctrl key shortcuts

Question

Environment: XUbuntu 13.04, Java: Oracle 7 u40 PyCharm 3.0 Community Edition 

Any shortcut which involves Ctrl key is not working. For example, I can Copy-Paste text using mouse or middle-button, but not via Ctrl+C/Ctrl+V. When I hover mouse in menu, I can see shortcut tooltip and Settings confirm that shortcut is correct. But it is not working.
Shortcuts with Alt, like Alt+F7 work normally.

Other apps, for example, Aptana studio - which is Java and Eclipse-based works normally. All system applications work with Ctrl button OK.

Answer 1

Probably IBus is messing with your Java keyboard shortcuts. Just do

killall ibus-daemon 

Answer 2

I was able to resolve my problem seemingly by rearranging my keyboard layouts on Debian, so that my English(US) keyboard was on top. I'm only putting this down as a answer because its a solution that is stuck in the comments section and not as an actual answer.