Windows 2008 R2 Domain Controller (PDC) - NTP server - time showing local CMOS clock

Question

I'm having issues setting an external source on a Windows 2008 R2 domain controller (PDC emulator role for the domain)
Here is the output showing its source is the Local CMOS clock.
C:\Windows\System32>w32tm /query /status
Leap Indicator: 0(no warning)
Stratum: 1 (primary reference - syncd by radio clock)
Precision: -6 (15.625ms per tick)
Root Delay: 0.0000000s
Root Dispersion: 10.0000000s
ReferenceId: 0x4C4F434C (source name:  "LOCL")
Last Successful Sync Time: 06/11/2014 15:44:15
Source: Local CMOS Clock
Poll Interval: 6 (64s)
1) I have performed the following on the DC with the PDC role:
net stop w32time
w32tm /config /syncfromflags:manual /manualpeerlist:"0.pool.ntp.org, 1.pool.ntp.org, 2.pool.ntp.org"
w32tm /config /reliable:yes
net start w32time
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)
AllowNonstandardModeCombinations: 1 (Local)
ResolvePeerBackoffMinutes: 15 (Local)
ResolvePeerBackoffMaxTimes: 7 (Local)
CompatibilityFlags: 2147483648 (Local)
EventLogFlags: 1 (Local)
LargeSampleSkew: 3 (Local)
SpecialPollInterval: 3600 (Local)
Type: NTP (Local)
NtpServer: 0.pool.ntp.org, 1.pool.ntp.org, 2.pool.ntp.org (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)
But still showing the output:
C:\Windows\System32>w32tm /query /status
Leap Indicator: 0(no warning)
Stratum: 1 (primary reference - syncd by radio clock)
Precision: -6 (15.625ms per tick)
Root Delay: 0.0000000s
Root Dispersion: 10.0000000s
ReferenceId: 0x4C4F434C (source name:  "LOCL")
Last Successful Sync Time: 06/11/2014 15:58:45
Source: Local CMOS Clock
Poll Interval: 6 (64s)
2. If I resync and rediscover the following error appears: 
w32tm /resync /rediscover 
Sending resync command to local computer
The computer did not resync because no time data was available.
3. I've also clearing the current time config, by
net stop w32time
w32tm /unregister
w32tm /register
net start w32time
But no change, it still shows the Local CMOS clock. 
4. This event is showing 
Log Name:      System
Source:        Microsoft-Windows-Time-Service
Date:          06/11/2014 15:43:30
Event ID:      12
Task Category: None
Level:         Warning
Keywords:      
User:          LOCAL SERVICE
Computer:      domaincontroller1
Description:
Time Provider NtpClient: This machine is configured to use the domain hierarchy to determine its time source, but it is the AD PDC emulator for the domain at the root of the forest, so there is no machine above it in the domain hierarchy to use as a time source.
It is recommended that you either configure a reliable time service in the root domain, or manually configure the AD PDC to synchronize with an external time source. Otherwise, this machine will function as the authoritative time source in the domain hierarchy.
If an external time source is not configured or used for this computer, you may choose to disable the NtpClient.
Event Xml:
<Event xmlns="http://schemas.microsoft.com/win/2004/08/events/event">
  <System>
    <Provider Name="Microsoft-Windows-Time-Service" Guid="{06EDCFEB-0FD0-4E53-ACCA-A6F8BBF81BCB}" />
    <EventID>12</EventID>
    <Version>0</Version>
    <Level>3</Level>
    <Task>0</Task>
    <Opcode>0</Opcode>
    <Keywords>0x8000000000000000</Keywords>
    <TimeCreated SystemTime="2014-11-06T15:43:30.465619200Z" />
    <EventRecordID>77295</EventRecordID>
    <Correlation />
    <Execution ProcessID="256" ThreadID="2056" />
    <Channel>System</Channel>
    <Computer>domaincontroller1</Computer>
    <Security UserID="SID" />
  </System>
  <EventData Name="TMP_EVENT_DOMAIN_HIERARCHY_ROOT">
  </EventData>
</Event>
5. If I perform the below it appears DC2 is having problems but I'm not sure if related. 
C:\w32tm /monitor
DC1.domain.local *** PDC ***[192.168.1.1:123]:
    ICMP: 0ms delay
    NTP: +0.0000000s offset from DC1.domain.local
        RefID: 'LOCL' [0x4C434F4C]
        Stratum: 1
DC2.domain.local[192.168.1.2:123]:
    ICMP: 0ms delay
    NTP: -110.4925481s offset from DC1.domain.local
        RefID: (unspecified / unsynchronized) [0x00000000]
        Stratum: 0
DC3.domain.local[192.168.2.1:123]:
    ICMP: 0ms delay
    NTP: -0.0256084s offset from DC1.domain.local
        RefID: DC1.domain.local [192.168.1.1]
        Stratum: 2
DC4.domain.local[192.168.2.4:123]:
    ICMP: 0ms delay
    NTP: -0.0011524s offset from DC1.domain.local
        RefID: 80.84.77.86.rev.sfr.net [86.77.84.80]
        Stratum: 2
Warning:
Reverse name resolution is best effort. It may not be
correct since RefID field in time packets differs across
NTP implementations and may not be using IP addresses.
Any help would be much appreciated. Thanks. 
Craig Brand

Answer 1

I suspected some issue with AV so uninstalled. 
To resolve the Access Denied I followed these steps: 
stop w32time
w32tm /unregister
reboot
regsvr32 /u w32time.dll
w32tm /register
sc query w32time -- you should see that the service is set to
shared mode -- this is presumably how it should be -- if you try to start right now, you'll get the expected 1290 SID-related error
reboot
w32time should now automatically start at boot up and be running -- that was my result -- it's running as shared, started on its own, and I can do the w32tm /query commands successfully
After rebooting the time service started. 
I then repeated the steps: 
net stop w32time
w32tm /config /syncfromflags:manual /manualpeerlist:"0.pool.ntp.org, 1.pool.ntp.org, 2.pool.ntp.org"
w32tm /config /reliable:yes
net start w32time
w32tm /query /configuration 
And all worked. I'll wait a short while to see if this fixes the issue. I also have am SA case with MS so will confirm fix when resolved. 
Craig Brand