No, no fix so far. I'm basically stuck as to what to try next. As far as I can see SCOM Agents and UR versions are all correct, MP is updated and I've tried re-creating the SCOM<->VMM connection with and without PRO enabled, but no change.
I've enabled the VMM debug log and VMM is definitely logging Microsoft.VirtualManager.EnterpriseManagement.Common.DiscoveryDataInvalidRelationshipSourceExceptionOM10 exceptions, but it doesn't give any information that I can determine about what object it is looking for (mind you the log is massive as this system isn't idle)
My current speculation is that the hypervisor cluster itself is not being correctly discovered by SCOM, so when VMM goes to find the objects it's expecting to be there for that cluster, they're not present. Indications in favour of this are that one of our hypervisor clusters is shown as "not monitored" in SCOM. Unfortunately, I don't know how to debug that process to see why it's not working as expected.