> I think that suggests there is a difference in the HW. If the two
> boards performed exactly the same, there should be no difference in
> the measured offset.
> 
> I'm not sure what that could be. Maybe the CPU is throttling due to
> high temperature? On x86_64 frequency scaling (power saving, turbo) is
> a major problem for phc2sys, causing unstable measurements and weird
> offsets.
That would seriously surprise me, considering it's just two (as far as I
can tell) identical Beaglebone Blacks, in the same room, sitting barely 20
cm apart.

I'll keep looking though, thanks for your help! I'll try and see if I can
cut out the system clocks and phc2sys entirely somehow.


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