W32TM keep pointing to CMOS clock instead of the NTP servers assigned in registry after service is restarted

Hello Folks,

I manage a very time sensitive environment of 2008 R2, 2012 R2, standalone (as in not domained) physical servers which need to sync to internal GPS provided NTP servers.  However I am running into an issue where the servers are not referencing the data for the NTP servers even though the details are located in the W32TM registry location.  

I have tied the Windows Time service to the Network service so the Time service does not stop using sc triggerinfo w32time start/networkon stop/networkoff

Changed the following reg values
HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\services\w32time\Config
AnnounceFlags to 5

w32tm /configure /syncfromflags:manual /manualpeerlist:ntp.internal.server.com,0x1 /update
w32tm /resync /rediscover

Before running "net stop w32time && net start w32time"
C:\Users\admin>w32tm /query /status
Leap Indicator: 0(no warning)
Stratum: 3 (secondary reference - syncd by (S)NTP)
Precision: -6 (15.625ms per tick)
Root Delay: 0.0319977s
Root Dispersion: 7.8016621s
ReferenceId: 0x0A3C810E (source IP:  10.60.129.14)
Last Successful Sync Time: 8/11/2014 10:52:54 PM
Source: ntp.internal.server.com,0x1
Poll Interval: 10 (1024s)

After running "net stop w32time && net start w32time"
C:\Users\admin>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: 8/11/2014 10:34:58 PM
Source: Local CMOS Clock
Poll Interval: 10 (1024s)

I feel like I am missing something here but I am not seeing what it is... PLEASE HELP!!
Daz19Asked:
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footechCommented:
I think that's an artifact of you using the /rediscover option with the /resync switch.
If your environment is really time sensitive (i.e. it requires high precision), then you're going to have to move away from using the W32time service.  One we use in our environment is NetTime.  http://www.timesynctool.com/
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Daz19Author Commented:
Thank you for responding footech,

I will review NetTime and give it a go to see how it works..

Regards,
Redchronos
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frankhelkCommented:
If you consider moving away from W32time (a good idea, because it's a crappy source of annoyance in NTP mode whenever I used it that way) you should try the real thing for NTP applications: A Windows port of the classic Unix NTP daemon.

A really mature thing (around for decades and still maintained), simple to install, easy to configure, works like a charm with the performance footprint of an ant and is stable as a rock.

See my article on NTP for details and don't hesitate to ask me if I left something unclear ..
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Daz19Author Commented:
Thanks folks for giving me feedback on how to correct this.  I figured out the issue was a shaky DNS resolution of the NTP host names because of the restrictions on the the network associated on one of the NICs.  A persistent routing rule cleared up the sync issues for me.
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