Same thing happened with my new 4000DVD. I put about 20 vids I converted from youttube...they worked.
Then I added about 50 more and only one(the first) video plays...to play anything else I need to use the iPod control itself, not through the touchscreen. If I try doing it that way, it blanks out the song, artist ...etc. and says "stopped"
DId you solve your problem? I've kinda given up, but if I can reformat(3rd or 4th time on my 5th gen 30gb) and it works, then I am good to go.
But I doubt it.
I also have about 20gb used on mine though.