I'm going to ask a stupid question, and I don't know anything about Macs, but it may solve your problem.
That question is: did you safely eject your iPod or did you just pull the plug ?
Maybe the information wasn't completely written on the hard drive and was still in the cache.
Personally, on my computer, which runs Linux, I have to right-click on my iPod's icon on the desktop and select "Eject". Then, I get a warning that pops up and that tells me there is still information being written on the iPod. It usually takes up to 1 minute once I ejected my iPod for all the information to be written on its hard drive. If I do not wait until the process is finished, there are some missing and/or broken files on my iPod.
Hope it may help,
Delta009