You might need to update WinAVR, as well. I'm only using AVR Studio 4.18, but when I upgraded from 4.13 after getting my Axon Mote, I had problems compiling, and updated WinAVR. I think... or else it was upgraded WinAVR and had to upgrade AVR Studio to fix it.
Alas, I'm not sure, and can't decipher the errors there, but thought I'd mention that possibility. (I'd also be curious to know if reinstalling 4.18 works... oh wait, what version of AVR Studio did you upgrade FROM, anyways?)