Ok, I've ruled out optimized meshes and textures being the problem. I'm thinking the cause could be one of two things:
1) BSA Timestamps. I unpacked/repacked all my BSA's and used OBMM to reset BSA Timestamps. All my BSA's are now dated 1/1/2006 12:00 am. Is it ok for them to all be dated the same?
2) I ran QTP3 Redimized meshes through PyFFI and textures through Optimizer Textures and then installed the optimized QTP3 Redimized archive with BAIN. I then uninstalled it which as far as I know removed the files, but could I have corrupted something by chance because of how Qarl's uses parallaxing?
These are all just guesses but I'm going with process of elimination. Any help here would be much appreciated.