Hi Dom,
This can happen when the SCOM Configuration Service gets 'out of sync' with our VMware objects.
The solution is to restart the SCOM Configuration Service on the RMS - however, I'd advise scheduling this outside business hours, as the RMS has to rebuild it's in-memory configuration for the whole environment. It does not cause a monitoring outage, however depending on the size of your monitored infrastructure it can put a load on the RMS, so it's best done outside normal business.
Note that improvements in the SCOM Configuration service in SCOM 2012 have resolved this issue
Cheers
Alec