I exported each m4v individually from their own sequences (and their own Premiere save file/project). The footage is 59.94fps, as is the Premiere timeline, and it is exported as a 29.97fps m4v video file. Reviewing the clips in the Encore timeline nothing is noticable cut off.
I created the Encore timeline the normal way, choosing Blu-ray as the format, 29.97 interlaced. Then I drop my clips in the timeline in the order I want them. It is exactly what I did last time when it worked perfectly.
Last night after playing around with Premiere and Encore some more, I took the Premiere timeline I made to export audio and tried dropping in the 5.1 wav files in the correct order. Exported that as one large 5.1 wav which I then converted to ac3. Plopped it into Encore, and almost success. It still goes out of sync, but it is not gradual, and I have isloated where it goes out of sync, and just have to figure out why and how to fix it. I'll try dropping my long 5.1 wav into Premiere and see if it goes out of sync there too. The easiest solution would be to shorten the audio clip in Premiere by a few frames and export it. Tonight I will give it a whirl. I'll get it eventually.
I am almost tempted to start using Premiere Elements. Much more limited, but also much easier.