Almost everyone here is having this problem, noone knows how to fix it, and Bioware either doesn't care or they are just to lazy to release a patch that will go through whatever is causing this problem, Reinstalling doesn't fix the problem.
Was this ever fixed? I think the issue is that if you have the patch before this installed it gives errors because some of the same files are being installed again since this patch has all patches up to this point in it. Anyway, just a thought. I hope something is found out soon since I can't use some mods unless the game is at the newest patch.