Some details would help ... iTunes exact version, platform etc. Have you updated iTunes or the ipod updater recently? I would suggest rebooting, turning only iTunes on and try to update it like that. Also try switching off Limewire integration in Limewire, although if Limewire is off, this should not make any difference, I think
The only way Limewire COULD have affected it imho, is if iTunes integration was switched on, and if LW was running.
I seem to recall I used to have a bit of a problem loading my iPod with other things running on the computer. Since a change in everything related. It will now update in any conditions.