So as I mentioned earlier I decided to re-colaborate for my black version in case I accidently chose the least common Timer0, only to get the exact same Timer0 the second time, that is C7C.
I've since tried to Rng Cobalion again. I've noticed that when I do the chatot flips the pitches in the game match those on the main window in the RNGreporter, which apparently means that I hit my seed. Yet when I catch Cobalion I keep getting the wrong IVs.
So I tested catching Cobalion without doing the chatot flips only to get the same wrong pokemon, and doing the chatot flips but stopping short just to see if maybe the Initial PIDRNG frame was off a bit but again I got the same wrong pokemon.