I have been having this issue for a while, and it only became a problem recently when I needed to boot into Windows 7 for work quickly and could not. I have a MacPro with 2 hard drives: one has OS X, the other has Windows 7. I can run Boot Camp just fine, and I can run Windows 7 in Parallels just fine, but after I've run the partition in the VM at least once (and always shut down properly), the next time I boot into Windows 7 it does a hard drive check and finds some messed up file descriptors and fixes them. After that Windows 7 seems to be fine until I run in Parallels again. The file check takes a really long time (20-30 minutes, depending on how much it thinks is messed up) so it is getting annoying. Has anybody else seen this? Is there a way to fix it? I am running the latest Parallels 6 and keep my Windows 7 partition up to date. I am running the latest Snow Leopard as well. I'm going to try setting up two hardware profiles, one for Boot Camp and one for Parallels, to see if it helps at all.
