When you check the files in the regular launcher and close, they will remain active until you open that part again.
Maybe its just me , but ive never experienced that. To unactivate any Mod/DLC in the game launcher. I would have to open then uncheck.
I did experience this happening to my DLC's one time, where they would always uncheck them selves. (this was after reinstall of game but didnt put the second disk in) Cuz it seemed to show they were there. However the guts of the files were not there so it kept doing that.
So Im just guessing this behavior with the Game launcher is a symptom of the mods not being installed correctly???