Unless you copied the files over to the iPod in disk mode, I wouldn't consider having the music on your iPod a "backup." While it's possible to use programs to extract the music back off of an iPod and into iTunes, it's relatively simply to make a mistake and sync your iPod with an empty iTunes library and completely decimate your "backup" in a matter of seconds.lI have backed up all music files on an ipod...
So... is there a problem you'd like help with, or was the error message you got that one, single time just concerning?...but today itunes seems to be working fine.