The double folders thing is troubling. It shouldn't be like that.
Did you use LSTools to unpak the folders? And did you place the unpakked files into your main game directory? If so, that might be causing the doubling issue, as the game may read from both the .pak file and the unpakked files. I don't know enough about it to say so with any certainty however. Maybe someone else could offer a bit more reliable insight.
