i had the same problem. try this link :
http://www.hackint0sh.org/f205/76361.htm

however, after i got my phone to work again, my backup doesnt seem to work. ( the iphone would hang each time during reboot ( stuck at progress bar ) ) .
- still finding a way to 'read' my backup hehe.

p/s: well, at least i got my phone working back lol. as far as i know, there's no jb for 3.1 yet on windows.