Hi all!
I had same problem. Then I scanned all my tracks with mp3val utility and realized that all my skipped mp3 tracks had problem like this:
WARNING: "D:\Music\Musicals & Rock Operas\Funny Girl (1968)\01 - Overture.mp3" (offset 0x8d9c): MPEG stream error, resynchronized successfully
I fixed these tracks with mp3val, cleared all songs on iPod and resyncronized it (it's important! If you just repair files thay will not be updated on iPod by iTunes, so you have to re-upload them to your gadget). Now it works like a charm!
PS I mentioned this problem few months ago. One day after syncronization lots of my mp3's stopped playing on iPod classic 80GB (although they kept playing in WinAmp, iTunes and other desktop software as usual). I thought it was a start of the HDD end, and bought a new iPod classic 160GB. When I syncronized it to iTunes library, I was shocked getting the same problem!!! Then I started investigation and found solution described above. Hope it shall help.