Although I suppose a timing/sync problem with clock slippage **might**
> be the culprit, it's funny that it only manifests itself twice a day
> rather than constantly [for severe uncontrolled slips] or at
> evenly-spaced intervals throughout the day & night [for less frequent > slips].
Your entire post is well done, but the above slightly misses the mark.
Big IF ... If one terminal is timed from a source traceable to a Stratum 1 clock and the other terminal is clocked from an unsynchronized Stratum 3 clock, it would not be unusual to see the stated trouble pattern due to the long-term frequency drift rate of the Stratum 3 clock. I've fixed a few of these sync problems.
Don