I have had an ongoing issue with USB keyboards failing to work with Sonar.  A PC reboot always fixes the problem (as far as I know).
 
Although I do not know the cause, I did discover that unplugging or plugging in a USB drive will cause the problem 100% of the time.
 
For example, M-Audio keyboard works fine.  I change Passport USB drives in another USB port.  The keyboard no longer works.  I reboot the PC and the keyboard works.
 
Any ideas why this is happening?  The good news is that at least I can relate the issue to a specific action, although there could be other causes not yet identified.
 
Thanks.

Are you doing a "Safely Remove Hardware and Eject Media" or just pulling the plug? Are you powering down the drive before doing a 'safe' disconnect? Both of those might cause problems.
 

Just came across a few more tidbits (I've been trying to solve my own USB MIDI keyboard issues)...
 
- try unplugging all your USB devices except the MIDI keyboard, mouse and computer keyboard (if you're using USB mouse and computer keyboard)
- if your MIDI keyboard is plugged into a USB 3 slot, try it in a USB 2
- make sure you're using a reasonable quality USB cable
 
The solution for me was unplugging everything I wasn't using (printer, scanner, external drive).