I'm using a PicoScope 6404C together with a pulse/delay generator for the triggering. (PicoScope 188.8.131.522)
It seems there is an problem with the trigger input using the AUX IN channel.
Using the AUX IN as trigger source, the signals jitter by approx 6 ns, but the channels don't jitter relative to each other.
When I use channel A as trigger source, I don't see the jitter:
I tested this with two different pulse/delay generators with different TTL signal voltages (0.5 V to 2 V amplitude) and the standard of 5 V.