To test the issues, export from Premiere (not dynamic link) using the MPEG2-DVD preset. Use a sequence that is less than 10 minutes. That will create an m2v and a wav (or a3c, if you select dolby at that step - I usually leave it for Encore).
In Encore, create a new project, and import "as timeline" the m2v/wav (select both). In the Project Panel, look at the "DVD Transcode Status" column. Does it say "Don't Transcode"?
Do you hear all the audio in Encore preview?
Confirm Encore CS6? And confirm you are starting with an HD source and HD Premiere sequence?