Having the same issue with my kC now. The pitch is badly off and sounds majorly sour. As far as 44.1 vs. 48, I'm at 44.1 and this did not change when the pitch decided to wank out.
On my keyboard there is no Config menu, though there is a Master Tune in the System settings. I tried the "Master Tune at -63" trick and many of the other suggestions here, pitch is still off. The only thing I can think of is that I remember using the keyboard Pitch Bend wheel sometime before the pitch fell apart, but this shouldn't have changed the entire tuning of the instrument by itself, no? (The wheel is not stuck, either...)
Running Mac OSX Mavericks 10.9.5 (this is not new either... none of it is) on a 2014 iMac, using Ableton Live 9 with Virus as an external instrument. Virus is running OS 5.5.
Guess I'll go make some non-Virus music for now. 
Grateful in advance for any advice.