The Funk fills are also affected on somes songs, It’s not a desync or whatever, just the fills
I don’t know if this will help at all but I can share my thoughts. I upgraded an RC50 to the Infinity 3 looper (for the sound quality? - I am seriously now considering replacing that with the Aeros).
In my setup, the PC (and whatever DAW is running) is the master clock. That goes to BB and from there to the looper. In the absence of any active clock coming from the PC, and as far as anything in the MIDI chain after the BB is concerned, the clock coming from the BB is the master. That to me is logical and makes total sense.
So on my looper and on all my effects units for that matter, I only listen for the sync and ignore all other MIDI data. So I set them to ‘sync only’.
Routing is so important and can be quite complex but rewarding if done properly.