So ntpd has been behaving reasonably well with the snprintf fix. I had good results with only internet servers. My PPS and SHM refclocks were set to noselect.

I removed the noselect on the PPS refclock and left flag3 set to zero (no kernel discipline).

Everything seemed fine and then:

Sat Feb 11 01:12:10 PST 2012
     remote           refid      st t when poll reach   delay   offset  jitter
==============================================================================
x127.127.22.0    .PPS.            0 l    -   16  377    0.000  -111.40 351.464
 127.127.28.0    .GPSD.           4 l   49  128  377    0.000  -14655. 2814.64
 169.229.70.201  169.229.128.214  3 u  103  512  377   39.347  -9274.2 6597.61
 72.14.179.211   127.67.113.92    2 u   79  512  377   57.746  -14699. 10685.0
 24.124.0.251    132.236.56.250   3 u  521  512  377   77.930  -9835.0 7451.10
 130.207.165.28  130.207.244.240  2 u  153  512  377   79.131  -9155.6 6554.15
 131.144.4.10    130.207.244.240  2 u  142  512  377   86.537  -9102.3 6526.3

This occurred very suddenly (over the course of only 30 seconds). The clockstats show the offset wandering in cycles going up to 1 second and down to -1 second. This happened within a few hours of starting ntpd with the PPS enabled.

I'm not sure what happened.  But when I restart ntpd:

11 Feb 09:17:17 ntpd[6823]: 0.0.0.0 c61c 0c clock_step -16.611482 s
11 Feb 09:17:01 ntpd[6823]: 0.0.0.0 c615 05 clock_sync

and the offsets calm down (this is just moments after restarting the jitter and offsets are continuing to drop down to their former values of about 1-2ms or better):
     remote           refid      st t when poll reach   delay   offset  jitter
==============================================================================
x127.127.22.0    .PPS.            0 l   12   16   17    0.000  -27.265  16.503
 127.127.28.0    .GPSD.           4 l   75  128    1    0.000  -16595.   0.122
 69.65.40.29     209.51.161.238   2 u    2   64    1   74.261  -16.396   2.797
+169.229.70.201  169.229.128.214  3 u   37   64    1   37.577  -33.420  12.747
*198.137.202.16  69.36.224.15     2 u   35   64    1   36.607  -32.686  12.116
 130.207.165.28  130.207.244.240  2 u    9   64    3   77.754  -20.400  11.968
 131.144.4.10    130.207.244.240  2 u    9   64    3   85.509  -17.853   7.143

The actual PPS signal coming into the system is extremely stable. The jitter remained below 100us for several days straight (reported by clockstats while PPS was in noselect).

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