Does anyone else have problems with mods mysteriously disappearing? I blame it on wrye mash, but in reality, I have no idea.
It's really the only thing turning me off Morrowind right now. 20 or so of my favorite mods (plus the meshes/textures) have been destroyed, like I never downloaded them.
actually, some meshes from mods I still have are missing as well... This has put me into the habit of backing up, but only the recent 2 or 3 mods I've gotten.

Does anyone else have access to the computer?

no. Neither have I moved the files.

What is your OS and where have you installed MW? Seems like it might be better for vista/win7 to install outside of program files.

vista, program files
do I have to reinstall to change the location?

While I am unsure of what would be causing this, it sounds like a virus I once saw which its only purpose was to mess with people by randomly moving files around the computer. Not that this is a virus though.

It is a virus, it's called Vista.

Vista uses some... interesting... protection in the program files directory. It actually, in part, mirrors the directory and doesn't let you see the real thing.

What you'll want to do is find Morrowind (Program Files\Bethesda Softworks\Morrowind) and cut the entire directory. Paste it to somewhere safe, like C:\Games\Morrowind or another hard-drive. Now, go into Users\[your name]\Application Data (IIRC) and find the Morrowind folder there. It should contain an INI and possibly some other files. Cut that and paste it into your new Morrowind location, so this INI over-writes the old one.

After that, Morrowind should work great. It's just not designed for Vista's ridiculous nonsense, so you have to give it a logically-functioning location.