I have a few suggestions for you today.
1st. try and sync a few songs at a time, 3000 songs at once can possibly freeze your pc.
2nd. try and reinstall itunes. : http://www.support.apple.com/kb/HT1925
how much memory is your Ipod?
1st already tried.
2nd did it as well
16GB. Yesterday it get on stuck also the second iPod in my possess, so I guess that is iTunes, but since I already installed it 2 times... could be possibible that is only the iTunes realease that have a bug? or maybe some fake preferences that are not removed once iTunes is unistalled normally?