Yes, there's another thread in the Encore forum about this but since it hit a dead end, maybe someone here in this forum can help since it's actually Premiere/AME causing the issue...
The problem is simple and it's cross-platform:
When you export a H264 Bluray file using the new Premiere 7.1 update (using AME Queue or Direct Export from Premiere) and drop that file into Encore CS6, it shows up as "Untranscoded" and Encore forces you to re-transcode it all over again a second time in order to burn it (you cannot manually switch it to "Don't Transcode"). Export the same exact project using the same exact settings through Premiere 7.0.1 and the resulting files show up in Encore as "Don't Transcode" so they don't get re-transcoded a second time.
Try it. It sucks. Any ideas?