Annoying problem if you rely 100% on keyboard shortcuts! I had the same problem and the fix is very easy. You will need to uninstall your keyboard driver and restart your computer and your CTRL keys will function once again. To do this:
1) Click Start
2) Control Panel
3) Printers and Other Hardware
4) Keyboard
5) In the Keyboard Properties window, click Hardware
6) Click Properties
7) Click Driver
8) Click Uninstall, click OK
9) Restart your Computer