I don't think that the standard Windows defrag would be much use since it merely re-connects the file elements but leaves the files in much the same place.
PerfectDisk (and similar programs) can also remove the spaces between files to compact the directory and that is when the files stuck up near the partition get moved down out of the way.
Lying awake in the early hours (as usual) it occcurred to me that every partition program I used had the option of creating an emergency boot disk so you could carry out repairs when it all went tits up. This put a copy of the program on a bootable cd.
Perhaps you could create such a disk which would, of course, be running before Windows woke up so could work its magic without any interference?