I'm sure that you've heard horror stories about Win8, and as the official guinea pig here, I can confirm that it's DEFINITELY a big change. You can work around the annoyances, mostly, but I just found a biggie today.

I was setting up a little Morrowind testbed, and neither Morrowind itself OR Enchanted Editor work (so far). I'm not going to waste too much time sorting this out, but at least the CS functions (with errors).

Here's the error message from warnings.txt - one I've never seen before, and the BSAs seems sound:

Only one root object allowed on file "base_anim_female.1st.nif".
Make sure the object was exported without cameras.

If I try to launch the game, it CTDs shortly after the first render of the prison ship.

Stick with XP or 7 for now.

Rochndil, who hates compatibility-breaking...

I have no idea about any of that since I don't use Win8 and don't plan to. But that seems an odd error to receive, and doesn't seem related to incompatibility in your OS (like I said, I don't even count as a neophyte here, but just saying). Have you tried copying a file from an animation replacer or something into your data files yet?

With that said, I have NEVER seen that error either. Sounds very strange.

The first thing that pops into my head when I hear of new installs with files missing is the old Vista thing where all of the install files were not actually installed because Vista was actively blocking it. If the missing file is known to be inside a properly registered BSA, I'd try extracting and/or copying that BSA one more time to make sure it isn't corrupted.

Where is your Morrowind install? This could be an extension of the permissions issue first spotted in Vista/windows 7 - 64 bit.