Okay since this is apparently all the rage then I decided to just test it since I was fairly certain that I had no issues with my vampires skin... ever.
Current testing profile is.
Skyrim, Update, Dawnguard, Hearthfire, Dragonborn (esm´s) followed by USKP, UDGP, UDBP, UHFP (esp)
Extracted unofficial patches as priority over Optimized official HDDLC. Nothing in archives section of MO selected.
Issue is not present.
Tested on my main mod profile... Different skin textures for vampires so I did not expect any issues and there where none.
So must admit that I am confused about this issue! :)
Could you confirm that, as z9 suggested, you are extracting all BSAs - including the vanilla Skyrim and DLC BSAs?
I was going to post this in the other thread as a question, but I don't want to derail it with newbie-ish questions and I think you're doing exactly what I was thinking of doing:
Before I even knew about this newly-discovered issue with BSA extraction, I had been considering unpacking all my BSAs - including all the vanilla/DLC Skyrim BSAs. Not for any great purpose, but simply because I was interested to see all of vanilla Skyrim's assets appear in my Conflicts tab, and see exactly what mods were overwriting what files from the vanilla game, versus official DLCs, versus files newly added by mods.
I didn't actually do that, because I thought it would end up being too much noise in my Conflicts tab (nearly every mod would show a Conflict icon, where before I could use that icon to decide which ones I needed to review), and also because I wasn't 100% sure if there was any problem from doing that.
So now I want to ask: is that what you're doing? And therefore it's OK to do?
So: I convert my vanilla/official-DLC assets into MO mods - making one mod for Skyrim, another each for DG, DB, HF - and in those mod archives I include both the ESMs and the BSAs. Then I install those mods through MO, and it will extract those BSAs as normal. Thus the vanilla/DLC game content is treated identically to all my other mods: 100% loose files.
Then in my Mod load order, I interleave the vanilla Skrim/DLC 'mods' with the Unofficial patches - as indeed MO's "Potential mod order load problem" warning would likely tell me to do, based on the LOOT sorting. So my mod order would read: Skyrim, USKP, Dawnguard, UDGP, Hearthfires, UHFP, Dragonborn, UDBP, HD DLC, HD DLC Patch, <rest of my mods>
My entire game - vanilla, DLC and mods - would now be loose files, and loaded in an order defined only by MO. I would have 0 BSAs of any kind; my Archives tab would be empty (or all unchecked.)
So is that what you're doing? Are there any problems with doing that - besides having the extra clutter in the MO Conflicts tabs? Are you unpacking all the Skyrim BSA files too (e.g. Skyrim - Sounds.bsa, -Meshes.bsa, etc), or only the DLCs? You said you had nothing checked in Archives, so it sounds like all?
Thanks very much in advance!