Can you please detail exactly HOW you have things set up to where you are dealing with Kontakt being the master, presumably?
I simply load Kontakt into a project's synth rack, load one or more instruments into that instance, then insert audio and midi tracks in the Track Pane and make the routine assignments to pick up audio output from Kontakt and send the midi data for each Kontakt instrument to the appropriate midi channel assigned to each corresponding instrument.
So, please do explain how you have things configured for your attempts to get things to stay in sync. Thanks :)
Bob Bone