Here's my situation: I'm using Encore CS6, importing files made in PP CC. When I encode DVD files and import three clips, lay them on the timeline, make a menu and author a DVD, the audio works fine. When I encode the same three clips as blu-ray MPEGs and import then into Encore and put them on the timeline, the first clip has audio; the second and third do not. Two notes: when I preview or scrub the timeline, the audio works fine on all clips, when I burn the BD, it only shows up on the first clip. Second note: I imported clip one as a timeline; I may have imported clips two and three as an asset. I can't recall for sure.
Could that make a difference? I could start over, but these blu-ray discs aren't the cheapest thing in the world and the less trial and error, the better.
Thanks!