It would appear the ABS system wants to save something to the ECU, but is not able to do so due to some sort of configuration issue that I have not done correctly.
When I use VCDS to clear the ABS error with the car running, it stays away until the engine is turned off. Then if ignition is turned on again, and the engine is not even started the ABS error comes back still.
This issue didnt happen till after I upgraded to V3 and had to build a map from scratch, so I am sure its something I have just overlooked.
Turned out to be engine protection settings. I was able to do a compare with an A3 R32 base map and discovered through trial and error that turning off all engine protection warnings somehow fixed the ESP/ABS issue.