Update:
I have no idea if this was a one time bug, but after going through everything over again, I flipped the master off and back on again and the AP started working. I know with I didn't turn it off and for this plane I have everything on the alpha\bravo disabled so that wasn't an accidental switch off.
I'm sure it was some how my fault, but in case someone else runs into this despite everything looking A-OK, maybe this will help?
Cheers