I'm generating QT Reference movies out of Avid Xpress HD. Sometimes Encore 2.0 want to do an audio comform upon import, sometimes no. Anyone know what triggers audio conform. I tried to set PCM instead of Dolby in the prefs, but no joy.
Have you checked your timecodes? If you only export parts of your timeline, TC will not start at zero, which is what it should be (within a PGC [or "timeline" as Encore calls them], timecode can only start at 00:00:00:00). Encore will read those TCs from QT and audio files.
Also check your project and export setting in XPress. Sometimes it will mess up its own settings and (seemingly) use odd sample rates e.g. things like 46264 Hz on a 48000 kHz project 8-O). It does not really use the wrong settings (files will be properly 48 kHz), but it goes out of sync and embeds this wrong info into exported files. This is a sporadic problem and can oftentimes be fixed by restarting the computer.