Oddly enough, after flashing an 8800gt from my first gen mac pro to work in my '09 I experienced similar behavior in that it works great under OS X but I can no longer use it through boot camp.
I just reflashed my EVGA 8800GT that was running the EFI32 bit ROM and in my MP 2x2.66 Quad (MacPro1,1) to the EFI64 bit ROM and put it in my new 2x2.8ghz Octo (MacPro3,1) and it works fine in OSX and Bootcamp with XP.
Curious, maybe the 8800GT won't work in the '09 Mac Pro. I don't know of anyone else who has tried the 8800GT in the '09 Mac Pro.
I'm done with the 4870 flashing. I'll get the official Apple 4870 when it's available.
Tried 2 cards and both failed, so I'm done.