I rebuilt chrony with --enable-debug and ran with -d -d Below is some output although I'm not 100% sure what it means. Tried looking at the source code to see if I could ascertain the cause but I was unable. I let it run for a bit and here's some sample output. The pattern just seems to repeat over and over.
2017-11-14T20:34:08Z refclock.c:765:(filter_add_sample) filter sample 0 t=1510691647.698064095 offset=-0.198064096 dispersion=0.000001833
2017-11-14T20:34:08Z refclock.c:520:(RCL_AddCookedPulse) refclock pulse ignored offset=0.003574796 sync=0 dist=1.500000000
2017-11-14T20:34:09Z refclock.c:765:(filter_add_sample) filter sample 1 t=1510691649.560963143 offset=-0.060963144 dispersion=0.000001833
2017-11-14T20:34:09Z refclock.c:520:(RCL_AddCookedPulse) refclock pulse ignored offset=0.003580218 sync=0 dist=1.500000000
2017-11-14T20:34:10Z refclock_shm.c:104:(shm_poll) SHM sample ignored mode=1 count=1202298 valid=0
2017-11-14T20:34:10Z refclock.c:520:(RCL_AddCookedPulse) refclock pulse ignored offset=0.003583732 sync=0 dist=1.500000000
2017-11-14T20:34:11Z refclock.c:765:(filter_add_sample) filter sample 2 t=1510691651.549839364 offset=-0.049839365 dispersion=0.000001833
2017-11-14T20:34:11Z refclock.c:520:(RCL_AddCookedPulse) refclock pulse ignored offset=0.003582173 sync=0 dist=1.500000000
2017-11-14T20:34:12Z refclock_shm.c:104:(shm_poll) SHM sample ignored mode=1 count=1202302 valid=0
2017-11-14T20:34:12Z refclock.c:520:(RCL_AddCookedPulse) refclock pulse ignored offset=0.003574833 sync=0 dist=1.500000000
2017-11-14T20:34:13Z refclock.c:765:(filter_add_sample) filter sample 3 t=1510691653.564970804 offset=-0.064970805 dispersion=0.000001833
2017-11-14T20:34:13Z refclock.c:520:(RCL_AddCookedPulse) refclock pulse ignored offset=0.003576043 sync=0 dist=1.500000000
2017-11-14T20:34:14Z refclock_shm.c:104:(shm_poll) SHM sample ignored mode=1 count=1202306 valid=0
2017-11-14T20:34:14Z refclock.c:520:(RCL_AddCookedPulse) refclock pulse ignored offset=0.003574430 sync=0 dist=1.500000000
2017-11-14T20:34:15Z refclock.c:765:(filter_add_sample) filter sample 4 t=1510691654.612400335 offset=-0.112400336 dispersion=0.000001833
2017-11-14T20:34:15Z refclock.c:520:(RCL_AddCookedPulse) refclock pulse ignored offset=0.003573701 sync=0 dist=1.500000000
2017-11-14T20:34:16Z refclock.c:765:(filter_add_sample) filter sample 5 t=1510691656.599152919 offset=-0.099152920 dispersion=0.000001833
2017-11-14T20:34:16Z refclock.c:520:(RCL_AddCookedPulse) refclock pulse ignored offset=0.003564191 sync=0 dist=1.500000000
2017-11-14T20:34:17Z refclock.c:765:(filter_add_sample) filter sample 6 t=1510691657.519233732 offset=-0.019233733 dispersion=0.000001833
2017-11-14T20:34:17Z refclock.c:520:(RCL_AddCookedPulse) refclock pulse ignored offset=0.003540440 sync=0 dist=1.500000000
2017-11-14T20:34:18Z refclock.c:765:(filter_add_sample) filter sample 7 t=1510691658.565950335 offset=-0.065950336 dispersion=0.000001833
2017-11-14T20:34:18Z refclock.c:520:(RCL_AddCookedPulse) refclock pulse ignored offset=0.003555990 sync=0 dist=1.500000000
2017-11-14T20:34:19Z refclock.c:765:(filter_add_sample) filter sample 8 t=1510691659.612487851 offset=-0.112487852 dispersion=0.000001833
2017-11-14T20:34:19Z refclock.c:520:(RCL_AddCookedPulse) refclock pulse ignored offset=0.003554507 sync=0 dist=1.500000000
2017-11-14T20:34:20Z refclock_shm.c:104:(shm_poll) SHM sample ignored mode=1 count=1202318 valid=0
2017-11-14T20:34:20Z refclock.c:520:(RCL_AddCookedPulse) refclock pulse ignored offset=0..003536535 sync=0 dist=1.500000000
2017-11-14T20:34:21Z refclock.c:765:(filter_add_sample) filter sample 9 t=1510691661.556102500 offset=-0.056102501 dispersion=0.000001833
2017-11-14T20:34:21Z refclock.c:520:(RCL_AddCookedPulse) refclock pulse ignored offset=0.003563863 sync=0 dist=1.500000000
2017-11-14T20:34:22Z refclock.c:765:(filter_add_sample) filter sample 10 t=1510691662.603828315 offset=-0.103828316 dispersion=0.000001833
2017-11-14T20:34:22Z refclock.c:520:(RCL_AddCookedPulse) refclock pulse ignored offset=0.003559951 sync=0 dist=1.500000000
2017-11-14T20:34:23Z refclock_shm.c:104:(shm_poll) SHM sample ignored mode=1 count=1202324 valid=0
2017-11-14T20:34:23Z sources.c:356:(SRC_AccumulateSample) ip=[NMEA] t=1510691656.723338336 ofs=0.080481 del=0.200000 disp=0.009623 str=0
2017-11-14T20:34:23Z sourcestats.c:583:(SST_DoNewRegression) off=1.007180e-01 freq=6.636850e-05 skew=3.159318e-04 n=16 bs=0 runs=10 asym=0.000000 arun=0