A bit of background first, I've read all the threads here about AI and MO for both Oblivion and Fallout 3/NV and tried all the methods.
I deleted my ini's, and recreated them through steam. All my tweaks are done through MO.
I took my old install which I don't want to reinstall because reasons, and made it it's own mod in MO with it's own profile. This install works perfectly fine outside of MO.
I do have 2 other basic profiles setup for modding and testing with vanilla that don't have any issues as far as I can tell.
Some textures don't work and some do which is very very strange, with either MO's AI, or using Quarn's or FOMM's AI method. I also tried the ArchiveInvalidated.txt generator which worked the best of the bunch, but I had purple textures sometimes (bodies, hands, loading screens, random). When it partially works it's very odd that rock textures and landscape will work, but the rock skirt texture will not even though they are in the same directory and BSA. I'm starting to think this is just a bug in MO.
It didn't matter if BSA management was on or off (I left it off after trying both), and all BSA's were checked. In the instance of MO's AI, it was at the top of the list.
I've also tried back dating all the bsa's with Better File Attributes and forward dating all the loose files/folders.
I've never had a problem with Skyrim, so I'm at a loss as to what to do.