Figured it out, it was messing with the high and low stops too which is what seemed odd..
Basically this is my third set of wheels. The bike originally came with mavic aksiums. I swapped over to some RS80s a year ago – cassette spacer and all. Just bought some tougher wheels based on hope hubs for training and some longer holidays I have planned. I also bought a new cassette.
The mavic spacers are 1.75mm and the standard shimano ones are 1mm. So my RS80s were running on the original 1.75mm spacer and my new wheels the 1mm spacer. Didn’t have anymore 1mm ones but did have a 1.75 in the bits box. My wheels will now be compatible with each other but no one elses until I can get a 1mm spacer.
I assume the 1.75mm spacer will be fine for now as I’ve run it for a thousand odd miles so far.