I have exactly your issue with Handbrake 0.9.6, I got this problem in 2 movies, I tried to play them many times but every time they stuck at same point. If you watch them with a PC everything is played fine.
If you pass the file obtained from handbrake in mkvmerge the movie seems to run well.
I don't use strange options in Handbrake, just ATV2 profile, mkv container, audio AAC faac (bitrate 160), subtitles vobsub with option "burned In" enabled and that's all.
What do you think guys, it's better to come back to the past versione 0.9.5 or "clean" the movies with mkvmerge?