Nope. Works fine before I do anything at all to it.
Although once I start changing things, it all seems to go side-ways in more ways than just this. After the third reinstall of the game (making sure to delete the Steam folders that stick around even after uninstalling through Steam), my first change was to try Flawless Widescreen. Worked perfectly the first time and then every time after that, it windows down to 800x600. I noticed that somewhere, somehow, before I'd even tried with Flawless changes, that 800x600 tga files are being put into the Override folder. Which is just odd as I have no idea where they're coming from and if I try and delete them, they come back after starting the game up again.
I've also noticed that the changes I first made to the swkotor.exe for the widescreen fix (changing compatibility mode) remain even after deletion and reinstall so I'm guessing that's something in Windows somewhere.
I dunno. At this point, after spending several hours over several days, trying to get this all to work, I'm thinking it's all just not worth it.