Finally, I see someone else is having the same problem.
Encore 6.0.1 update was to fix the audio going out of sync and was working great.
I did a Media Encoder update recently and my preview is fine on Encore but, when I play the Blu-Ray the audio is out of sync by 18 seconds too.
The Audio .AC3 file is 18 seconds longer than the Video H.264 Blu-Ray file I notice.
What is the fix Adobe!