I have just noticed the same problem. It seems to have started in the last month or so for me. I have tried shorter clips too but it still is an issue when running Melodyne 4 as a region FX in Sonar Platinum. Work perfectly in the past.
Makes editing on the fly almost impossible due to the melodyne time line running ahead of Sonar's.
Also experiencing some delay now between hitting the stop button (with the mouse) on the transport console and the track actually stopping. Feels like I just got sent back to the sync days of the 90's. Puzzling - what changes are causing this?
Mike