A couple of people have had trouble after updating to the latest iTunes, but that's just been a prob where the "LimeWire Tunes" playlist doesn't show up. You had this prob before updating iTunes I guess?
It sounds to me like it might be a problem with your iPod rather than with LW. Have you been to the iPod help site? Try the general fixes (in blue) & if they don't help there's a pretty good search function. They also have a forum I think.
http://www.apple.com/support/ipodmini/

(If you ever have troubles with the iTunes side of LW, like playlists not showing up, deleting the LW preferences can help. Points 2 & 3 here
Fixes for LimeWire)