Here is a crazy thought:
We know that players like the MyHD handle HDTVtoMPEG2's splice point discontinuities just fine, while other players don't.
Discontinuities are actually part of the MPEG-2 spec. Any fully compliant player should handle them fine - IF they're marked by setting the discontinuity bit. I imagine that HDTVtoMPEG2 is not setting this bit. I wonder if setting it would fix playback with some of those players that currently don't like HDTVtoMPEG2 streams - not making the splice point perfectly smooth, but at least letting the player play through the splice point without major problems like dropping the audio, audio going out of sync, or worse.
I don't mean to be a downer about Cris's recent efforts. If he can fix some of the problems that some players experience now, that's great. I'm just concerned that in doing so, the resulting streams might be less compliant than they are row, causing problems for players that have no problems now.