I am having an issue similar to the one Westhoff123 was having. When I run the patch it doesn't scale anything visually in the game menus but does seem to place the click targets for everything other than the main menu in the top left at 800x600 while the visual rendering still happens center frame. I can revert back using the backed up swkotor.bak.exe and everything works fine, but it's quite weird.
I am using the Steam version if that matters...