I used to have smcFanControl installed as well. Still do, but when I had a similar problem it only happened after long periods of time as well. When I would try to restart/shutdown an app would fail to quit and would prevent log out. If I force quit the app (typically the Finder), another would do the same, and so on until eventually I quit every app I could in the Activity Monitor, and the machine would seemingly logout but never proceed further.
It's possible that there is some combination of software failures/glitches happening after the machine is put to sleep several times that is causing this. As for the XP partition: maybe? I still have the same XP partition installed from Leopard, and I haven't had the same issue since upgrading to SL, but then again you said your was having problems anyway.
For starters you can try creating a new user (smc wouldn't open at login, and the preferences and settings would all be fresh and "clean"). Use that new user for a few days and try to get the same problem to happen again.
If the problem doesn't happen with that new user it's a good sign. If the problem does happen it isn't necessarily a bad sign. Either way, your end result might be performing a clean install, or at the very least an Archive and Install from a system disk. One of those methods would give you a better idea of whether or not it is software related.
The only reason I mention all of these methods is that you may end up spending as much time creating a new user and transferring over all of your data to it than just backing up and starting over fresh.
I'm assuming that you updated to SL or did a clean install but migrated your apps over. It's possible that some incompatible or outdated app transferred from your previous system caused this. If you end up starting over, I would suggest not migrating applications over, but instead redownloading and reinstalling whatever you can, and installing those other apps (that you can't dl) fresh only if there is confirmation that they work with SL or have an update that will allow them to.