We’re using AVID Adrenaline 1.6. We have tried using Encore 2.0 in the past. However, it must use a version of Quicktime that causes problem in the AVID.
We rolled back to 1.5. The problem there is that Encore has problems with reference files that A)contain audio and B)are over 15 minutes or so. The workaround from AVID is copy the sequence. Delete the audio from one. Export the reference with just the video. Then from the other sequence, export only the audio as a wav file.
In Encore, choose “import as timeline” and select both the ref file and the wav.
That’s how we are doing it. Don’t know if your problem is similar. Sounds like it.