I've had that happen to me too. It's been a while... I wish I could remember what caused it. Like, with a TV show, each episode is a Title, and then there might be a Title that's extra-long, which is what plays if you hit "Play All." It's actually a separate movie file.
But randomly adding part of the movie at the end...
I usually rip one Title: at a time, and for the movie file, try to pick the one with the length similar to what the movie actually is. I don't know if you're doing all the special commentary stuff, too.
More fun with Handbrake... The .mkv files Handbrake makes can play on an iPhone, but I use a preset to make them smaller, to conserve space: http://www.sendspace.com/file/w0r1uc
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But randomly adding part of the movie at the end...
I usually rip one Title: at a time, and for the movie file, try to pick the one with the length similar to what the movie actually is. I don't know if you're doing all the special commentary stuff, too.
More fun with Handbrake... The .mkv files Handbrake makes can play on an iPhone, but I use a preset to make them smaller, to conserve space:
http://www.sendspace.com/file/w0r1uc
Good luck!