Ableton Link in Traktor has been buggy for quite a while now... @Stevan may be able to help you.
I always forget which sync mode that Link has trouble keeping in time...
I really hope the Traktor team are able to spend some time on it this year after the mooted overhaul of other big features on the horizon. I've gone back to using MIDI clock in the past year or so, especially when it comes to DMX lighting or syncing my Maschine.
Let's hope changes are on the way.
How has the new Missing Link Junior been so far? Really want to get one soon.