A lot of times when I try to load the esm of new mods I get an error message saying the mods can't find the proper master files. When I check it out in the launcher, instead of Morrowind.esm I have MORROWIND.ESM. Same thing with Tribunal, Bloodmoon, better bodies and variants, IceBrady'Hurdy's robe replacer, etc. How do I fix that. I am now running the game on vista. I was running it a month ago on Windows 7 and was using the same exact mods, with the same exact download locations, but I didn't have that problem then. What's going on?

Chances are that the file creation dates of the .esm's have changed, wrye mash can fix the errors by resaving the .esp to the "newer" copyies of the .esm files, you can also do this manually by loading each .esp in the construction set as an active file and resaving it, only load 1 esp at a time if you are going to do it this way, tbqh though, its a pretty harmless warning and can just be ignored.

Also, if I launch Morrowind through Morrowind FPS Optimizer, none of the mods are applied to my game. i.e. tha game only loads Morrowind, Tribunal and Bloodmoon files. It doesn't even run the Morrowind Patch Project or the Morrowind code patch. It's nerver done that before either.

You don't need to launch the game through the FPS Opt.
As long as it's open, you can launch the game normally and it will do its job.

It doesn't. When I launch the game normaly, I cannot get my widescreen setting to work, (I use 1920x1200 resolution), but Better Bodies and Better Heads work, along with Seyda Neen Docks, and most of my other mods that have the master file thing right.
However, none of the new textures work that way (I am using Morrowind visual pack v3.0 and many of Darknut's textures, and others)

If I launch the game through the FPSopt, none of the mods work but the new textures are all there. Also, only certain aspects of the Morrowind Code Patch work under FPSopt, such as the permanent disposition change after bartering, but the trap door that's supposed to be in Seyda Neen isn't there. Same thing with the Morrowind Patch Project stuff, some is there, some isn't. These two work normaly if I launch the game normaly though.

I've been trying to figure it all out for a while now. Reinstalling everything from scratch didn't do it. So I'm rather lost here.

The problem is your file location for morrowind, I'm assuming you have installed in c:\program files\

You will want to move that install location...make it c:\games or something, just get it out of program files.

when thats done, right click the launcher, the morrowind.exe, and the fps opt. and set them to always run as administrator, that will solve your UAC headaches that you are getting now.

I cannot do that, or cannot see how. Normaly when you install, the installer asks you where to install the program, but in this case, the pathway is preset to c\program files\bethesda softworks\Morrowind, and I cannot change it. It goes from the license agreement screen to the confirmation screen where it says it will install there. Says click back to change the pathway, but it never actually gives me that option. Once again, this only happens on my vista run computer. Under Win7 or others I have never had that problem.

Actually, you can do that, just right click your "bethesda" folder, copy, paste where ever you want(as long as its not in program files or any subfolders in program files), then uninstall morrowind normally, now, go to your new location which won't have been removed by the uninstall, and run morrowind, it should work fine, you will need to reset your resolution settings in order to create the registry paths, but it should work...thats how I moved my morrowind copy anyway.

Matilija is right. Windows 7 and vista don't play nice when a file is in the "program files" directory. Also, dunno if this is related to your situation but if you are using MGE, it doesn't always run (and thus you see normal MW) if you use a shortcut or launch from another program.

ST