I have this exact issue.
Traktor scratch pro2 latest version
Latest version of the djm T1 and the firmware on the mixer is up to date as well
using windows 10. I haven't noticed the freezing when using the djm-t1 with windows audio, but i notice it all the time while mixing... music freezes and then when it resumes if the tracks were in sync, they resume out of sync.
REALLY annoying. and i doubt ill get support from pioneer on this.