Had a proper look at the shifting, which has not been great since changing the derailer. Hanger alignment was good, but i was still getting issues with cable tension, if tensioned enough to shift cleanly from five to four then it wouldn't shift from three to four.
Looking around I realised something I hadn't thought about before. This bike has horizontal dropouts, and an integral hanger. My previous derailer had a claw mount, so the axle can't reach the back of the dropout.
The new dérailleur goes into the hanger, so I had pushed the axle all the way back, so the pivot of the dérailleur was forward of the axle. Moving the axle forward, to the position it would have been with a claw mounted dérailleur fixed the problem, and shifting is now restored.