The VI setup is a bit complex (Was using a RT loop from a DAQmx card outputting a 1s rising edge to a PXI trigger line as my test input to the 6683). I would have expected a very steady 1s interval on the 6683H timestamps under any circumstances. I'm only reading the timestamps using the Max test panel (Not a vi)
When I sync my 6683 to a very steady PPS, the test timestamps are very steady.
When I sync my 6683 to my real PPS (With the jitter) there's essentially the same jitter in the test timestamps. If anything I would have thought the steadyness of the test timestamps would drift around slowly, but not at the level of the PPS jitter. More to a gentle precession around the jitter long term stability. It's almost like the 6683H is simply resetting its onboard clock to the second boundary on each PPS rising edge rather than drifting the clock like NI-TimeSync (or NTP) would. I sincerely hope that isn't the case because that would guarentee discrete jumps in timestamp accuracy which could skew even short term measurements.
As for a better PPS. The PPS is just a vxWorks CPU outputting a GPIO. vxWorks is running at a 4kHz rate thus the +/-250us jitter. On average though, the wakeup is spot-on to within about 20us (Interrupts etc). I don't have control over that design.