Yes, I’ve had all the problems like this too using CHR on Virtualbox. Nobody answered my previous thread about it.
The time difference gets worse with every VM boot, but restarting the host machine seems to reset it to only a small value in to the future. It is still wrong though.
The ‘solution’ to the Dude database problem is to disable it before rebooting, then re-enable it after the NTP client has put the time right.