[Peter Tysoe]

Weve been looking for a solution to this as well.
I find it utterly amazing that Prem CS5.5 doesnt do something as basic as encoding the chapter markers into mp4/m4v for video podcasts !!
Currently fiddling with iSubtitle on MAC,it doesnt re-encode just adds the metadata (but encoding and editting on PC)

Also not been able to save/edit/import chapter markers (so you coudl atleast automated the adding in iSubtile) or cut/paste markers between timelines is a pain. In audition you can at least export to xml. Adobe sort it please.

So, sorry no solution that I have found..yet.
Post here if you do find one.
Cheers,