In the VM's configuration on the host, you can enable or disable controlling the guest's clock. That's that only other thing I can think to check.
Also try finding a local timeserver (or two) and using that instead of the pool servers. The way the pool works, each system can get different servers at any time. There is no consistancy there for comparison.
EDIT: Also, you said "stock ntpd from packages". Did you install NTPd from packages or do you mean the base openntpd?
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