When I started using CS3 2 years ago I had some difficulty with the interface between PPro and ENCORE. I’ve also had sync problems when I import the sound and video seperatly into ENCORE. I have had NO problem since I began rendering out, using the PPro encoder, to MPEG-DVD and selecting the Multiplexing option in the Audio Tab. That should render out as a single file which you can import into ENCORE project panel. Open a time line, drag in the file and I’m sure the audio will be fine.
If you are already doing that, then I really don’t know what to check, but it sounds like you are describing ‘peaking’ audio so you may want to see if there is some feature to select, or deselect, regarding normalized audio.
