I'm encountering the same exact problem
I kkrull !
I have the same keyboard bug than you on my MacBook C2D : when booting under Win XP using a Boot Camp partition (NTFS), the keyboard sometimes isn't recognized. I must power off my laptop and try again, but even that sometimes isn't enough for getting the keyboard 'back' ...
On the contrary, when using the same Boot Camp partition with the latest beta of Parallels from inside OS X, the keyboard is always responsive...
Anyone has a solution and / or explanation to this ?
Thanks.