I have a solve for this issue. I had the same problem, ipod completely failed to read a number of tracks and skipped over them when on a playlist.
I did a number of different things which took about a week in total! But at least it cleaned up my collection in the process (My collection is 16,000+ songs). All looking very sexy, retagged, all album artworked and squeaky clean playback.
I first went through and followed the advice on the internet on the issue - checked tracks for errors with special software, played through the first few seconds of all the tracks on the ipod in itunes using a macro program to quicken the process, reset the ipod, restored the ipod, redownloaded itunes, reimported all the music into itunes nothing seemed to work!
So what I did that worked. I downloaded a program called DPPoweramp (its free). I imported all my MP3's (mostly youtube rips) and converted and re-encoded them into the .m4a apple lossless version. This takes half a day to convert and the lossless file quality is much higher but so is the file size. I also used DPPoweramp to cut out silence from the tracks and to 'normalize' the sound - although I don't think this would have had an affect on the ability to play on the ipod, just creates a nicer finish while doing the same process.
Once I had all the .m4a files, I reimported into itunes (I had to do this piecemeal because itunes kept crashing!). Although better quality my library was now too big for my 160gb ipod. So when syncronizing I have to reconvert the songs to an ACC (256k) quality so they fit. On hindsight this could have been done while importing these tracks into itunes through 'itunes import settings' and selecting in what format I wanted tracks imported as this would have significantly reduced synchronisation time (which also kept crashing!), however now I have extremely high quality tracks in my itunes.
Waallah, all tracks play perfectly on the ipod and the problem is solved! Best of luck with yours 😀
Now I have a question, why is itunes/ipod so sluggish, frustrating and unituitive to function - and why is there no real competition to the ipod on the market, which is a relatively simple technological product?