Hi Aarik, actually I managed to resolve this on my own last night and today.
I tried verify/repair, but it didn't change things. I then uninstalled and noticed that some directories of the game remained. When I tried to delete them manually I got an error "Error 0x80070091: The directory is not empty". I googled that error and it turned out I needed to run a ScanDisk for errors on the hard drive. My HDD is about 5 years old, so I was suspicious of it anyway.
I ran the check last night and installed the game again today. It's now working normally. I'm buying a new HDD Monday though