srt subs
This doesn't exactly answer your question, but if you can get hold of subtitles in .srt- or .sub-format instead, you can add them to your movie with Submerge, takes a minute or so, no reencoding.
I used to add subs in QT with Perian and then reencode them for ATV wit VisualHub, that took 22 hours for a 45 min show om my 3 GHz iMac. Converting for ATV without subs takes 2 hours, adding subs after 1 minute and I can disable the sub in QT if I'd like.