Sorry for the delayed reply, work has been kicking my butt the past few days.
Anyway, installing the game on a completely different drive fixed the issue. I did exactly as you mentioned and still couldn't get the issue to resolve itself, even after uninstalling the game and completely deleting any left over files in the common folder. There was something I was missing that was causing the issue, but in the end I still don't know where the issue stemmed from. Installing on a new drive fixed the issue though, so at least this isn't going to continue to bug me.
Of course, now I get to install mods one-by-one to see if one of those was the base cause despite the fact that I had deleted all of my mods previously and still had missing textures.