Unexplained timing (NTP) issues on systems connecting to Active Directory

Issue

• We're seeing unexplainable issues with the system clock jumping around. The ntpd will appear to sync at some point and then the time will jump and ntpq reports a huge amount jitter along with a crazy new offset. It's almost like something else is changing the time.

  [root@localhost]# date; hwclock; service ntpd stop; ntpd -qg; date; hwclock; service ntpd start; sleep 30; ntpq -pn; sleep 150; echo -e "-------------\n0+2.5 minutes"; date; hwclock; ntpq -pn;sleep 150; echo -e "-------------\n0+5 minutes"; date; hwclock; ntpq -pn; sleep 300; echo -e "-------------\n0+10 minutes"; date; hwclock; ntpq -pn
  Thu Jul 26 15:24:26 EDT 2012
  Thu 26 Jul 2012 03:32:59 PM EDT  -0.938183 seconds
  Shutting down ntpd: [  OK  ]
  ntpd: time set +511.401889s
  Thu Jul 26 15:33:05 EDT 2012
  Thu 26 Jul 2012 03:33:07 PM EDT  -0.867189 seconds
  Starting ntpd: [  OK  ]
       remote           refid      st t when poll reach   delay   offset  jitter
  ==============================================================================
   192.168.19.71   .GPS.            1 u   29   64    1    0.605    0.002   0.001
   192.168.19.72   .GPS.            1 u   28   64    1    0.511   -0.047   0.001
  -------------
  0+2.5 minutes
  Thu Jul 26 15:36:06 EDT 2012
  Thu 26 Jul 2012 03:36:08 PM EDT  -0.958181 seconds
       remote           refid      st t when poll reach   delay   offset  jitter
  ==============================================================================
   192.168.19.71   .GPS.            1 u   50   64    7    0.605    0.002   0.120
   192.168.19.72   .GPS.            1 u   52   64    7    0.511   -0.047   0.265
  -------------
  0+5 minutes
  Thu Jul 26 15:30:06 EDT 2012
  Thu 26 Jul 2012 03:38:39 PM EDT  -0.988382 seconds
       remote           refid      st t when poll reach   delay   offset  jitter
  ==============================================================================
   192.168.19.71   .GPS.            1 u    9   64   77    0.605    0.002 323419.
  *192.168.19.72   .GPS.            1 u    9   64   77    0.511   -0.047 323419.
  -------------
  0+10 minutes
  Thu Jul 26 15:35:07 EDT 2012
  Thu 26 Jul 2012 03:43:40 PM EDT  -0.991733 seconds
       remote           refid      st t when poll reach   delay   offset  jitter
  ==============================================================================
   192.168.19.71   .GPS.            1 u   57   64  377    0.762  511370. 273338.
   192.168.19.72   .GPS.            1 u   50   64  377    0.857  511370. 273338.