Update:

I have checked and rechecked, the sample rate is 44.1K in both apps.

Maybe I'm not using jBridge the right way. Can anyone post a screen shot of how the configuration is supposed to be setup in Options/Midi for Jbridge and Pianoteq? or Sampletank 3? I'm starting to think I have jbridge set to play on all the midi channels, and it is phasing with my Thru track......
Thoughts????