I had a similar problem and one very dull day I went through half of my 24GB, 4000+ song library and discovered around 10% of songs were being skipped straight over by my 2009 160GB ipod classic and others were playing halfway through and then stopping.
Until I found this thread I couldn't find a fix. I repaired the disk in disk utility and then restored it in itunes back to factory settings. I then added all the music back on the ipod, one letter of the alphabet at a time (that was a few hours wasted!) After going through 1% of my library, I've come across no problems so far, I think it may have been fixed!!
Only other thing that may have attributed to this is that I had previously stored all my music on an external HDD, and recently upgraded my mac to 1TB and moved all my music back across. I wonder if somewhere between the external hdd and the ipod it was corrupting the files??
Only issue I've come across is its now showing an error in diag mode when I run the HDSMARTData test, it worked before... any ideas anyone??