Is the Octatrack your master clock, and if not are you syncing it to a DAW and is your MIDI interface USB?
I’ve never gotten tight enough clock from a USB MIDI interface to have loops play click-free on the OT, there’s always enough jitter to mess up the timing of the loop point, even if the sample itself is seamless. Even with time stretch on it doesn’t work for me. With the OT the master clock I can get completely seamless loops.
Basically, the jitter from the external clock is enough that the actual timing of the trig on the flex track will be off by a few samples every time, and it won’t be consistent so it’s hard or impossible to compensate for, depending on the material. Adding a short fade out at the end of your loop in the audio editor helps but it won’t sound good on some material.
At this point I just don’t use external clock for the OT under any circumstances. It’s stable enough that it stays in time with the DAW really well (I’ve recorded 2-3 Octatrack driven sessions on Ninjam every week since since April averaging around 90 minutes and haven’t had any noticeable drift yet) so I use it as the master clock for all of my hardware, set it to the same tempo as the DAW, and send start and stop from the DAW. It works way better that way, even with a USAMO. The Octatrack just doesn’t work well with external clock even if its a very stable one.