Finally got this resolved after multiple tier escalations at my webhost. Outcome, they couldn't replicate it and said it was an issue with CPanel WHM and didn't seem to want to raise it with Virtuozzo as I'd requested, I can't do it as I'm just the end client. Instead they offered to migrate me to a new Virtuozzo container. It fixed it, and we won't discuss the 2 days of grief and inconvenience that followed. I'm sorry this won't help anyone here.
On the other hand, I have to say the CPanel support team were excellent, super fast replies and escalations and genuinely helpful (like the forum staff!). They were able to verify the issue and believed it was related to the Virtuozzo container's system status API that provides the stats to WHM.