I've had this problem 3 times before and long before I used Defraggler (since I've only just started using it). Every time was just after using Chkdsk and every time under XP. I have been warned NEVER to use the /f switch with it because it's downright dangerous unless reformatting your drive was an intention anyway. I never use it at all now, Partition Magic has a much better version that's more intuitive. XP did have a problem initially with drive management messing up the partition tables, it wouldn't surprise me if M$ have still not fully fixed this problem.
I have just used Defraggler on my 149gb C drive under Vista Home but have yet to reboot. I use 3 other drives for data so killing the C drive doesn't worry me, it's probably the best drive to test on for me. Also, I'm dumping Vista soon, since it's slow and pretty useless, overweight piece of crap as far as I'm concerned. Going back to XP so it would be no great loss if I had to do it slightly sooner than planned.
I have a laptop so I'll let you know what happens when I reboot. I really don't forsee any problems right now, other disk checkers built into Partition Magic have reported nothing unusual and certainly no raw partitions. Defragging free space right now so it will be probably an hour or so before I reboot, that's something I wanted to add to a wishlist, the ability to defrag free space at the same time as a file defrag.
Edit: Returned from a reboot with no problems. My system is running marginallly faster and has no corruption of any files.