How's the quality, and what were your compression settings? I've been playing around with iPod conversion a bit recently, and I'm still trying to figure out what works best -- especially with something like your films, which include lots of text to read.
What's the problem with the last frame? Is it just not finishing the conversion? I've found that sometimes, conversion software will say that all the time has elapsed for the project, but it actually has a while longer to go before the conversion is complete. I don't know Handbrake, so I don't know if it tells you what precise moment in the video it is converting, but if it does, it's possible that that conversion time estimate was off, and everything else is just catching up.
. . . but maybe that's not the situation at all.
Take care,
Sojourn