I have the steam version of Morrowind GOTY. I've disabled the in-game community, and am trying to get Morrowind FPS Optimizer to change my resolution, and I figured that out, but it doesn't apply the new resolution. I've tried launching it through steam, and the mfpso but I can't get the resolution I want. Any ideas why it isn't working?

Try using the resolution changer in MGE or use the http://planetelderscrolls.gamespy.com/View.php?view=Utilities.Detail&id=64.

Launch the game once and go to 'Options => Video' set a resolution at random, and quit the game.
Then launch FPS Optimizer and set your resolution that you want.