If you're still having trouble with v3, you should try the v5 release. I was talking to one of my collegues a bit more about your problem, and he said there was a bug they fixed where MIDI Clock ticks were sometimes being dropped. I'm not sure if this was fixed in the v3 or the v5 release, but dropping ticks would certainly cause some drift… Also, the v5 TimeFactor release has some big improvements to the Looper algorithm, and the v5 releases let you connect Factor pedals to H9 Control in case you need a preset librarian (https://www.eventideaudio.com/products/software/bluetooth/h9-control).
