I just ran into a similar problem with a 90 minute long file which just stopped about 10 minutes before the end. I ended up using Audacity to split it into 2 seperate MP3s. The data was there it just wouldn't play beyond a certain point for some reason.
I love my video iPod, I've just started converting all my 'Buffy the Vampire Slayer' and 'Firefly' DVDs to a format I can play on my iPod. It makes the hours I spend windowing eggs and collecting embryos just fly by.
One of my friends recently brought a car with an 'aux' jack so he could just plug his iPod in directly with a stereo to stereo lead, that was the first time I'd seen what seems like such an obvious thing to have.