This problem appeared after I updated to 4.0, then dissappeared in another update, but have now come back. Ctrl, alt and the shift key at least doesn't work, maybe others too. Since I use parallels for system administration and our new password policy requires caps and special characters I am now unable to log into my "PC" because of this.
trui, Are you using any kind of custom key mapping? If so, have you tried switching to defaults in Preferences - > Keyboard and Mouse? If that does not work, you can try make custom remaps of Ctrl in Mac to Ctrl in Windows, and so on, as a workaround. Also, could you please post the type of keyboaed you are using?
I have no custom mappings, and I tried to reset everything to default with no luck, I'm using a plain white mac keyboard. I can try one of the new flat ones and see if that helps. Strange thing is that it worked for a few hours earlier this week, and then when I quit and restarted parallels it was back to the usual keyboardproblem again.
I have now tried to remap ctrl -> ctrl, shift -> shift and so on, and that didn't work. the new flat mac keyboards don't work either. I connected a standard windows USB keyboard and connected to the virtual machine only, and this works, so at least I am now able to access my PC.
If there are problems, please navigate to Parallels Desktop - Preferences - Keyboard - and click Restore Defaults
Please, try the workaround presented here: http://forum.parallels.com/showpost.php?p=135069&postcount=17