I can't remember DX:IW (the horror) well enough to know whether setting the .ini files to read only will fix it (I seem to remember that some of the UT engine games needed that) but...
No, I already tried that. It fixes the resolution in the main menu permanently, but when loading a game, the resolution resets. As far as I know, each new or saved game actually has its own user settings.... and so, user.ini actually is only good for the rotating DX logo, LOL.
But even if I figured out a way to edit a saved game's user settings to fix the resolution, there's still the problem of it resetting every damn time I load a new level. I've browsed every single Deus Ex forum I know of, and I seem to be the only person in the world to have this problem..... it's just so damn weird. And I hate having to hate this game, since when it first came out, I was one of its few supporters among the hardcore DX fanbase.