Seems strange.. I doubt ProTools has anything to do with it.. Maybe try on the Apple forums.
Maybe if you reinstalled windows... In other words, add your 3rd partition, then delete and reinstall the bootcamp/XP partition.. If you're a regular windoze user then you should be used to having to reinstall windoze every time something goes wrong.... Ah I'm JK..
You do know that you should not record to the system drive, right? Doesn't matter that it's a partition. You should have an external FW drive..