After a massive headache of running through the game with my GF trying to figure out these buggy discovery achievements we finally found a solution and may help find a way to fix the bug.
We had every single location discovered on both normal and TVHM yet none of the achievements were unlocked for us.
Our last ditch effort was to try and explore every single location again on our characters without closing the game to see if that would somehow be a magic fix and what do you know it was.
We started with Pandora and the Hundred Names for Sand achievement. About half way through the zones my GF crashes and we decide to push on instead of starting from the beginning (in my head this was almost a perfect way to test my theory). When we got to the final location the achievement unlocked for me but it didn’t for her, pointing to the fact that her game was shut down in the middle of the exploration causing some of the discovery progress to not properly be saved.
Long winded story but this seems to be a major issue that I haven’t found a working solution to, figured I’d throw out some of my discoveries.
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have you tried doing it with a 100% clean new character?