Does the mod comes with a preference folder included? I mean the one that saves the preferences regarding video, audio and so on settings of the person who made the mod. If it does(and there`s no reason no to) then you could try removing that preference sub-forum and let your game generate it again. If it`s absent it gets spawned again everytime you start up the game. I had problems(though not like yours) a few times because of different resolution settings or something like this which my own system didn`t like.