I'd suggest starting a case here with product support.
https://support.serviceshub.microsoft.com/supportforbusiness
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I have 1- PDC which has all role holds and 3 Additional DC.
PDC- Win 2008 R2 Ent
ADC- Win 2008 R2 Ent
ADC -DC01-Win2k12 R2
ADC-DC02-Win2k12 R2
I have External NTP Server. Our PDC - sync time from this NTP server.
PDC:- source of NTP is our NTP server. Configuration of PDC is..
C:\Users\administrator.IDMC>w32tm /query /configuration
[Configuration]
EventLogFlags: 2 (Local)
AnnounceFlags: 5 (Local)
TimeJumpAuditOffset: 28800 (Local)
MinPollInterval: 6 (Local)
MaxPollInterval: 10 (Local)
MaxNegPhaseCorrection: 172800 (Local)
MaxPosPhaseCorrection: 172800 (Local)
MaxAllowedPhaseOffset: 300 (Local)
FrequencyCorrectRate: 4 (Local)
PollAdjustFactor: 5 (Local)
LargePhaseOffset: 50000000 (Local)
SpikeWatchPeriod: 900 (Local)
LocalClockDispersion: 10 (Local)
HoldPeriod: 5 (Local)
PhaseCorrectRate: 7 (Local)
UpdateInterval: 100 (Local)
[TimeProviders]
NtpClient (Local)
DllName: C:\Windows\system32\w32time.dll (Local)
Enabled: 1 (Local)
InputProvider: 1 (Local)
CrossSiteSyncFlags: 2 (Local)
AllowNonstandardModeCombinations: 1 (Local)
ResolvePeerBackoffMinutes: 15 (Local)
ResolvePeerBackoffMaxTimes: 7 (Local)
CompatibilityFlags: 2147483648 (Local)
EventLogFlags: 1 (Local)
LargeSampleSkew: 3 (Local)
SpecialPollInterval: 3600 (Local)
Type: NT5DS (Local)
NtpServer (Local)
DllName: C:\Windows\system32\w32time.dll (Local)
Enabled: 1 (Local)
InputProvider: 0 (Local)
AllowNonstandardModeCombinations: 1 (Local)
VMICTimeProvider (Local)
DllName: C:\Windows\System32\vmictimeprovider.dll (Local)
Enabled: 1 (Local)
InputProvider: 1 (Local)
In Additional DC - Time Sync source is Free-running System Clock. Other DC -1 & DC-2 Sync time from ADC which source is not NTP or PDC.
in ADC-1
C:\Users\administrator.IDMC>w32tm /query /configuration
[Configuration]
EventLogFlags: 2 (Local)
AnnounceFlags: 5 (Local)
TimeJumpAuditOffset: 28800 (Local)
MinPollInterval: 6 (Local)
MaxPollInterval: 10 (Local)
MaxNegPhaseCorrection: 172800 (Local)
MaxPosPhaseCorrection: 172800 (Local)
MaxAllowedPhaseOffset: 300 (Local)
FrequencyCorrectRate: 4 (Local)
PollAdjustFactor: 5 (Local)
LargePhaseOffset: 50000000 (Local)
SpikeWatchPeriod: 900 (Local)
LocalClockDispersion: 10 (Local)
HoldPeriod: 5 (Local)
PhaseCorrectRate: 7 (Local)
UpdateInterval: 100 (Local)
[TimeProviders]
NtpClient (Local)
DllName: C:\Windows\system32\w32time.dll (Local)
Enabled: 1 (Local)
InputProvider: 1 (Local)
CrossSiteSyncFlags: 2 (Local)
AllowNonstandardModeCombinations: 1 (Local)
ResolvePeerBackoffMinutes: 15 (Local)
ResolvePeerBackoffMaxTimes: 7 (Local)
CompatibilityFlags: 2147483648 (Local)
EventLogFlags: 1 (Local)
LargeSampleSkew: 3 (Local)
SpecialPollInterval: 3600 (Local)
Type: NT5DS (Local)
NtpServer (Local)
DllName: C:\Windows\system32\w32time.dll (Local)
Enabled: 1 (Local)
InputProvider: 0 (Local)
AllowNonstandardModeCombinations: 1 (Local)
VMICTimeProvider (Local)
DllName: C:\Windows\System32\vmictimeprovider.dll (Local)
Enabled: 1 (Local)
InputProvider: 1 (Local)
I'd suggest starting a case here with product support.
https://support.serviceshub.microsoft.com/supportforbusiness
--please don't forget to close up the thread here by marking answer if the reply is helpful--
I posted above the commands but it sounds like you may have some other issues. What's in the event logs? Sysvol and netlogon shares present?
Some general info
Might try resetting the problematic one.
w32tm /unregister
net stop w32time
w32tm /register
net start w32time
w32tm /config /syncfromflags:domhier /update
net stop w32time
net start w32time
then check
w32tm /query /source
w32tm /query /configuration
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