I learnt a mistake by virtualizing my Primary Domain Controller (PDC) emulator, which is the default master NTP clock on the Windows domain. PDC emulator is one for the five essential FSMO roles in maintaining the Microsoft Active Directory. Despite its misleading name PDC emulator for NT4.0, it is still used to support several AD operations, including being the default master NTP clock, password replication & DFS namespace meta data within the domain.
To find out which DC is the PDC emulator, run this on any DC: netdom query fsmo
The virtualized PDC seems to always "trust" Hyper-V time synchronization (part of Hyper-V integration service) more than the external NTP server (a Linux box), which I manually configured using w32tm (see this). Although the time was in-sync within the domain, it was out-of-sync with the real world.
Frustrated, I have to set aside a R200 1-U DELL server, run "dcpromo" and take over the PDC role. Finally, the clock is in sync. To sync the rest of domain controllers on VM, you've got to shutdown the VMs, turn off the time synchronization service on the Hyper-V integration setting and boot them up one-by-one.
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