Sometimes the results of a project change when it is re-rendered, even if the output format is the same. When you noticed the problem in the MPEG version, you may also have tweaked some of the transitions or sequences that gave you the problems. In other words, the improvement you witnessed in the AVC BD might be perfectly true, but have nothing to do with the format per se.
What bitrates did you use in the respective versions?
Do you notice any quality differences between the AVC and MPEG disc versions of rapid action or pan shots? I saw jitters or jerks (as if skipped frames) in AVC dusc images that were smoother in the MPEG versions at 17 mbps or higher.
I would like to think that a AVCHD video source burned to AVC would be better (or at least loss-less) compared to a conversion to MPEG, but my exports or burns to HDV-MPEG2 or a BD-MPEG somehow look better, even without bumping up the bitrate a lot. Conversion is out of the question for a 4.7GB disc, but the 25 GB space on a BD-SL gives enough space to accept the larger size of the MPEG output.