Linux – Why aren’t Azure Linux VM’s keeping time sync with host

From your description, it sounds like there is an actual hardware problem with the RTC (http://en.wikipedia.org/wiki/Real-time_clock) on the motherboard of server S2.

The Hyper-V guest gets it's clock initially from the host (HYV1), but as you have Hyper-V time sync disabled, it gets all further clock updates from NIST (which is working fine). Your Linux VM is not integrated with Hyper-V, so it is getting it's time from the domain, which is also working fine. Your other physical machines are working fine, it is just a single physical server that is having 1 second of drift every 20 seconds (which is a crazy amount of drift). The time is drifting much quicker than the network time sync can reset the clock to the right time (which if I recall correctly takes place every 8 hours).

If you want to rule out Hyper-V as a cause for the error on S2, create a "no Hypervisor" boot entry, reboot without Hyper-V, and see if the time drift persists. Instructions here: http://blogs.msdn.com/virtual_pc_guy/archive/2008/04/14/creating-a-no-hypervisor-boot-entry.aspx

-Sean

Try using pool.ntp.org instead. It's a more accurate clock. You could also try software called NetTime which is a better tool than the built-in sync.