@peter > Are you using Traktor 1 or Traktor 2? The DJM-900 only works properly with Traktor 2.
It should be in the Traktor Manual on how to test and calibrate timecode within the Traktor software, and could you please check out Pulse's video and make sure everything is correct and the same:
DJM-900 Nexus & Traktor 2 setup for timecode control
I'm not sure what you mean by "syncronising the above set-up so that disruption is minimal"?