Audio goes out of sync when Blu-ray folder is exported from Encore CS6

I compile a project in Encore using H.264 and .wav files. The audio plays fine directly from the timeline. It also plays fine when I preview it from Encore. When I finally export it as a set of Blu-ray folders, the audio exports out of sync with the video. It is approximately 6-7 seconds ahead of the video. What am I doing incorrectly? When I mux the files into an .MKV, the video is in sync with the audio so I know the files themselves do not have different start times.
I am running with an HP Z820 with Windows 7, 64-bit OS and 16GB RAM.

For anyone who's interested, I found a solution to this problem. Once imported into Encore, the leader in on the video and audio files cannot be trimmed at all. (I had been trimming the beginning of the video and matching audio file to eliminate the 8 seconds of dead space at the start of the clips.) Although the trim took effect immediately in the Encore timeline and I could also watch it in preview in sync, exporting was another story. The audio track seems to retain the trim when exporting but the video track does not, hence the 6-7 second delay between audio and video.
I reimported the files to my project and left in the 8 seconds of dead space at the start and voila! The video and audio match up when exported.
Ideally the trim tool would just work as its supposed to through export and all, but at least I found a solution I can work with.
(As a note, the trim works just fine in export on Encore CS5. I only had this problem with Encore CS6.)

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