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.
Probably IBus is messing with your Java keyboard shortcuts. Just do
killall ibus-daemon