Itunes is ****

[essexboy]

check that you have all the boxes on the left hand side ticked dude sometime you might have un-clicked them and hence it wont include on the transfer to ipod

[Zeus]

I've not heard of this being a problem before.

1) Backup your library into an XML file and back up all songs from iTunes libary
2) Uninstall iTunes, restore your iPod to factory default.
3) Reinstall iTunes
4) Dump the music into your iTunes library folder.
5) import your library XML file to pickup all music (providing it's stored in the same directory).

Select manually manage music option.