(In case of confusion, I started a new discussion here given that I narrowed the problem down further. Was http://forums.adobe.com/thread/1153451?tstart=0)
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 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 on the PC, but on the PS3 the audio is gone and video has this pulsating hiccup behavior, very weird. This occurs for either VBR 1-pass, or VBR 2-pass, but not CBR.
Other data points: I tried lower field order just for fun, no change in behavior. However, CBR is ok, but VBR 1-pass or VBR 2-pass both have this issue.
I do not understand why the result would vary based on queue vs. export with a sequence from PP CS6. And why CBR is ok, but either VBR variant is not.
Thoughts?