Right, the fact that it happens to MC and nothing else means that it does have something to do with MC, but not necessarily is it MC's fault.
I'd try the following:
First off, remove MC, and then remove any mention of it in the registry (be careful here and only do this if you're confident in editing the registry, or else you could be rebuilding your whole system.) Then reboot.
Then re-install MC and rebuild db as Jim suggested, in quarters or even smaller increments. Test each time afterward, as you could be looking for a corrupt file or files.
If your files are MP3's with ID3V2 tags, turn off tagging in MC (Options|General| Uncheck "update tags when file info changes".)
Turn off and unload from taskman (and make sure tray doesn't have open) any type of software that either checks the net automatically over certain intervals (such as Outlook, NAV, clock synchronizers, auto updates, server connections etc) or runs auto-backups or parsing on the current system. Get them all out there, anything even remotely suspicious in that type of behaviour should be gone.
Then test as you go, loading up any type of app that does this and wait for the problem to occur again.
Sorry, I wish it was easier, but you'll need to be thorough in rooting out the evil spirits that haunt your system.