Yeah, I'm a bit annoyed by this too.
The "ENCODED WITH: UNKNOWN" is definitely not the problem in my case. The files are perfectly valid MP3s and iTunes correctly shows them as encode with lame.
Besides, it doesn't affect whole albums for me, but definitely more 50% of the tracks.
I just re-encoded an album which had 7 of 11 tracks failing on the iPod. I used the exact same process as originally (lame 3.97, picard, mp3gain). Interestingly all tracks worked then.
I then restored the iPod and mass-imported my whole library again. Now the tracks don't work anymore again. So there might be some problem with mass-importing. (The files on the iPod disk still seem to be OK though, they still work everywhere but on the iPod).
I've submitted a lengthy bug report via
http://www.apple.com/feedback/ipod.html , but I doubt I'll get some feedback from that.