Recently I deployed a 2008 R2 Domain Controller running off VMware vSphere with VMware tools installed. I had found out that the VMware tools had Time synchronization with ESX host enabled (which the ESX hosts did not have ntp configured properly) and thus threw the DC's time sync way off. As a note it is best practice to either use only one of the time synchronization methods with DC's..... either all use Sync with ESX host or all use w32time...from my experience w32time seems to work better.
After discovering the time sync with esx host was checked I ended up getting lots of event errors 34 and 50 in the event logs. The fix was to uncheck the Sync with ESX host and edit the following Registry keys to allow me to sync the time back beyond the allowed sync change thresholds:
[HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Services\W32Time\Config]
MaxAllowedPhaseOffset 0xffffffff
MaxPosPhaseCorrection 0xffffffff
MaxNegPhaseCorrection 0xffffffff
After changing those keys I ran the following script and everything was fixed. :)
NET TIME /DOMAIN:<your domain> /SET
w32tm /config /update
w32tm /config /manualpeerlist:<your PDCe DC>
w32tm /config /syncfromflags:domhier /update
net stop w32time && net start w32time
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