This sounds familiar.....
I have/had the exact same issue, same iPod as well.
On my 60gb ipod video i never had this issue tho, so i think it's something to do with the 5.5g and up firmware (does it on my iphone too).
some songs will end very early, some play fine, others end 10 seconds into the song. all play fine in itunes.
When i had my 5g video and iphone, i played a problem track on both. I usually noticed some type of sound imperfection on the audio at the same point the track on the iphone would end. So i assume it had something to do with how it was ripped.
Does this ever happen with a track downloaded from itunes? I have bought exactly one album from itunes ever, and that was last month, most of the rest of my 40gb music collection was ripped. I assume there was an issue in the ripping process. Most of my collection was ripped with musicmatch, back before i had an iPod (or a mac for that matter).
Every time I find a track that has a problem, it's usally a problem with numerous tracks from that same album. So my solution is, i'll take the mp3 tracks and make a new CD using Toast. I use a CD-RW. Note I DON'T use itunes to burn the CD, it will still have the problem (i tried). Then I delete the mp3 tracks from both itunes and the computer, and re-import from the CD. Then i go back to toast and erase the CD-RW. I've never had a problem with a track after using this method, and I waste no CDs (just time). Since my library is so big, I only do this as i come across a problem track. Works for me.
When this first happened i looked for others with this prob, i was amazed that I found nothing. I've had this problem ever since the 1G iphone came out.
I never use ratings, play count, etc so all those stats mean nothing to me. If there's an easier solution, I'd sure like to hear it.
P.S.- I just realized how old this thread is. Never saw it before.