Issues with encoding in AME vs. PP CS 6 ...

I have an .avi file with SD 720x480i LFF 29.97fps .9091 originally edited from miniDV material.  If I place that clip in an 1080i sequence and export with the H.264 Blu-ray format 1080i UFF 29.97fps and select multiplexing to produce an .m2t file and export it plays fine on my PC and my PS3.  I tried as-is and also another variant with scale to frame.   However, if I pull that same file into AME, select the the same format and match the same preset settings, then export a .m2t that resultant file plays ok, but on my PS3 there is no audio and video has this weird stutter effect over the whole frame.   (The same thing happens if I start with a .mpeg format file with the same video characteristics.)
Please ignore the why are you putting SD into HD, etc. topic, that's not the point and I can go into the details if really necessary.   What I'm confused about is why I'm getting different results.   Is there some sort of magic that is occuring dropping into a 1080i sequence first before exporting out of PP CS6?   Or something else that I need to do in AME?
PS The reason I'm asking is I that have 57 files covering twelve years of home video I was hoping to batch convert to the above format for primary playback on PS3, PC secondary, without discs.

Ignore everything above just read from here.   The problem has been reproduced and simplified exporting from PP CS 6 only ...
I have a number of AVI and MPEG files that are SD 720x480i, lower, 29.97fps, PAR .9091.   Please ignore why I am doing the following for now.  If I create a new sequence using the AVCHD 1080i30 (60i) preset, drop in this footage with no other edits, then choose export to H.264 Blu-ray 1080i with audio multiplexing to produce an .m2t file, leaving all other settings default the resultant file plays just fine on my PC with several media players and my PS3.   However, if the only thing I do differently is  queue (vs. export) from PP, then the start encode button in AME, the resultant file plays ok only on some media players on the PC and on the PS3 the audio is gone and video has this pulsating hiccup behavior, very weird.   Not that his occurs for either VBR 1-pass or VBR 2-pass, but not CBR.
I do not understand why the result would vary based on queue vs. export working with a sequence from within PP CS6.    And why CBR is ok, but either VBR variant is not.
Thoughts?
PS Jeff: I thought the situation was different enough from the prior that it warranted a new discussion thread.    New readers will now go through several screens of information that can be skipped.

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