I don't really know why it is working for me and not for you guys, here is what I do:
start SWTOR-file-changer, restore backup, wait for it to finish. This puts your SWTOR back to non-modded state,
Then I launch the game patcher (SWTOR Launcher), log in as normal, if it doesn't have a patch to download and install then I click on "start changing files" on the SWTOR-file-changer, wait for it to complete, then click Play on the launcher and that is it.
Note that I'm not having the mod replace very many textures in the game - it only removes some of the armors, notably the "energy" armor or the underwear armor, there are a couple others that it affects, but not very many and that might be the difference. I deliberately didn't have it set to remove a lot of the armors, that is why I posted my settings file as that pretty much lists what is affected.