Well I've cracked it! It was in the services (see the original starting post, now edited).
I'm not out of the woods yet. Does anyone have a list of critically advised services for an operational Windows? I've enabled Themes, Desktop Management and Networking so far, but I'm still lacking things like troubleshooting and System Restore. Is there a list of processes I should enable without all the crap?
I haven't tried this after disabling the services, but System Restore seems to be at fault. As mentioned in an earlier post: "When shutting down, SR runs and I get the message "System Restore is complete." after it's done it's loading, and then on booting back up to the desktop I get an error message saying it couldn't transfer a file (not always the same one)."