I don't know why but my AC3 footage (1080i) with 6 channels is converted into DD stereo, Any idea why? I had done other Blu-Rays before that did not have this problem and are with 5.1 sound.
Encore cannot create 5.1 audio, all it can do is pass through compliant 5.1 streams. So..make sure your stream is compliant before importing into Encore and that you get a Do Not Transcode for it.