I may have stumbled across something....
I placed the VMs into Maintenance using Environment Overview (Inventory Explorer) and the alerts cleared as expected. (Previously, stopping collection either by the solution/adapter or individual VM object did not clear the alert which confused me)
I then ended the Maintenance and the alerts have not resurfaced. Metrics all appear to be collecting ok so I'm now hopefully that this has fixed the problem.
Let me know if this helps you as well!
Paul