I am having the same problem. I'm syncing the Time Factor to an Alesis Micron running sequences, and if I use the repeat switch to make a loop on the Time Factor, it will slide ahead of the Micron within 4 or 5 measures. I checked the updater, and I have the newest firmware.
I've been working around this, but it would be great if a future update could achieve tighter sync. Midi clock sync and the repeat switch were actually the main reasons I bought this pedal.