I have the same issue here an at least 5 installations at different customers on mine. It seems to make no difference if VC is running in a VM or on a physical Server, if VCDB is MSDE or MSSQL, if time is synced or not - always the same.
Anyway it seems to be an issue in the chart display. It shows as peaks that drop down to zero. But if i zoom in the relevant time window, it sometimes show missing values but if a change the time window again, the chart is there.
It is not really affecting the VM but really annoying to explain the customer.
I am thinking about opening a case with VMWare