Audio audible in one Encore timline, but not the other?

Hello,
I'm trying to troubleshoot an issue in an Encore timeline for Blu-ray with an MPEG-2 and AC3 file.  It's odd because with the exact same file specs for both video and audio, I'm able to hear the audio from test project timeline (shorter in duration), but not the full length project timeline (roughly an hour and half in duration).
I'm in the process of burning a disk to verfiy that the audio is simply not there, rather than a playback issue with the longer project, but can anyone suggest what might be failing here?  Again, the two projects appear to be identical in settings and file specs for video and audio, only the duration of one (working) is shorter than the other (not working).
The audio file has been validated outside of Encore as playing back audio.
Thanks for anything thoughts anyone might have here.  Btw, the project has no menu screens.  It is for a "play only" Blu-ray disk.
Mtbakerstu

Stan, thanks for the questions / feedback.
As it turns out the file specs were not identical !  No fault of Adobe- an ingest / encode application from another company mysteriously swapped out channels 1/2 of audio to 5/6, and were not readable in Encore.   This information was not readiliy accessible within Encore, but was discovered in bringing the audio into Final Cut Pro (where it could be heard).
Thanks again for your thoughts, as always.
Mtbakerstu

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