Hmm. Well, you could load your on-disk registry hives into Regedit.exe, and then unload them again. According to Smilin, I think, XP's Registry editor will "fix" any corruption issues when importing/exporting registry hives, but I don't know how well that applies to "live" hives that are being used by the system at the time. Regedit probably doesn't even let you load them seperately, now that I think about it.
I guess the other solution, is to attempt to find out what programs, services, drivers, etc. Are opening user-registry handles and not properly closing them during shutdown. I would check things like AV, firewall, and other resident programs first, and perhaps move on from there.
You might consider, deleting and re-creating whatever Scheduled Tasks that you have listed, I know that XP SP2 has made some changes in the area of Task Scheduler, perhaps there is some interaction with user credentials and the user registry, although that's somewhat speculation on my part.