System Preferences ->Keyboard and Mouse->keyboard shortcuts choose restore defaults.
If that doesn't help, I have had a few times where my keyboard shortcuts simply stop working for no reason. Logging out and then back in fixes the problem.
If you are referring to copy/paste/make new/close window etc, try using the command/apple key instead of the control key. Windows uses the control key as the modifier, while OS X uses the command/apple key.