Ahhh ... I was going to ask if that's the case.
From what I recall, there are actually two teams doing media playback for the PS3. One doing the BD/DVD (basically directed by the A-team from SCE), and another group doing the non disk-based media playback.
Given Sony's history, they may not even be in contact with each other (for some reason, I think the media playback team is from Europe or the US?) ... and it wouldn't surprise if they aren't even using the same libraries. The SCE team probably has custom decoders for MPEG2/4/VC1/etc. I never really did much testing since I have an external scaler, but there are probably IQ differences. Just look into the fact that there are several scaling options for MPEG2 DVD playback that don't exist for media files ... even VOBs.
With that in mind, it's quite possible it isn't a HW-based frame-reclocking at all (as a matter of fact, I certainly don't recall seeing something like that on the MoBo, unless it is embedded into another chip). I suspect it is a SW based feature that only exists for media playback. To some extent it makes sense. Look at PC-based media players versus DVD players ... it's a common feature in PC media players (SW players ala VNC, WMP, WinAmp, etc) ... but not common in DVD players. The mind-set of the SCE team was to port HW-based playback and add some extra features. Unfortunately, that feature list isn't necessarily the same as the other teams.
