As of now I feel for some reason the spread on RNG reporter for encounter slot, nature, ability, and gender is incorrect even though the chatot pitches match and I'm getting the right ivs. I'll probably try catching some at lower frames and seeing if the frame advancement is constant, but I don't think this is the problem.Hmm okay. Did you try hitting your seed and getting a Pokemon at lower frames? And are these exactly how RNGReporter listed them?
I also had a similiar problem like you where the frames around + the actual frame of my shiny frames always lead to the same PID which was not the shiny one. However, this only occured for frame over 1000 for me.
Perhaps someone else has some additional ideas which can cause the problem.
Update: I just doubled checked if I was getting crazy frame advances but now I don't think I am. I hit the seed and advanced to frame 80 and caught an impish level 26 Klink with plus. I then hit the seed again and advanced the frame to 81 and caught a relaxed, male, level 26 Joltik with unnerve. There are no two frames relatively adjacent to each other that can give these two pokemon.