Maybe a bug?
I entered a simple bass line, drum loop and piano part and let it loop so I could jam over it on the guitar and after a while it went all glitchy. This happened as clock master and clock slave. It doesn't happen after the same number of repeats and I've only encountered it on this tune and it takes a while. There is minimal other midi happening and the interface doesn't do anything strange so I doubt it's a bottleneck problem. It actually sounds quite cool so maybe this could be a feature, not a bug as they say. It could be the Genoqs version of the scatter found on the Roland TR8s...
I'm looking at the midi file and it certainly is glitchy. The only timing issue that I'm still experiencing is related to note ordering with the first beat, where sometimes the timing is slightly off. The v6 feature to give MIDI out B priority helped a lot so I haven't taken the time to figure that one out. I have run into very similar issues with my Mio10 MIDI router when there is a clock loop, i.e. the clock pulse MIDI is feeding back into the router. That eventually causes buffering issues. I also have some buggy gear that causes problems. My FutureRetro Orb occasionally sends garbage sysex/midi-cc data that the Octopus picks up as MCC and my Novation Superbass station always acts as a MIDI Thru, causing clock loops.
I don't see the problem you've posed and I record to my Octopus often with a lot of different machines with loops playing for long periods of time.