Why would an audio track cause a video glitch?

I have a 1080 60p clip with no audio.  If I create a sequence based on that clip, add a wav file to an audio track, then export using the H.264 60p custom preset with audio multiplexing to an .m2t everything looks fine.    However, if I export using the H.264 Blu-ray preset, 720p, 59.94, multiplexed, to an .m2t file the video has some stutters towards the end.   If I remove the audio track and do the same export, still muxed, the video is fine in 720p.   I get the same result if I start with a 720p sequence (i.e. addition of audio causes video glitch).  
Edit: tried a different audio file, this time .mp3, same problem.
Edit: importing the muxed 60p export with audio, then exporting as noted in 720p has the same issue.
Comments?   Let me know if what I'm describing isn't clear.

Hi Jim - understood in an ideal world one would have source video footage, sequence, and output target all the same.  Is it not common though for folks to have situations where there is more than one target output?
Anyway, I think I have a tree covering both roads if I understand your analogy.  What is wrong with the following picture?  I took the original 1080 60p clip, dragged it into a 720p 59.94 sequence, exported the video only.  The exported video looks just fine in this case.  I even tried different formats (Matrox MPEG I-Frame HD, H.264 Blu-ray muxed and not).  It is all good.
Next I imported the aformentioned no issue video that is in 720 59.94 into a sequence that matches then exported to a matching format.   No issue with the resultant video.   Is this scenario not what you mentioned?   Start with video that matches the sequence and target output?   
However, if I add an audio track, the video has some flashing/stuttering at the end particularly towards the top.   Why would exporting with or without an audio track in the above scenario make a difference?
In case it matters, the video came from a modified After Effects template.  I don't own AE and paid another guy to modify the template.  I will go back and ask him to render in 720p 59.94.  Still, the above just doesn't seem right. 

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