My G5 iPod often won't unmount after copying things to it from my PowerBook running 10.3.9, though I never have problems with my other Macintoshes running various other systems, or with my other iPods. I get a message saying that the iPod was being used by another application, even after all applications were closed, including restarting the Finder, and even after logging out and logging back in.
If you have the same problem, this is how to solve it, short of shutting down your computer. Put your computer to sleep, and then the iPod will unmount and you can safely disconnect it. This doesn't make sense to me, but it works.
Mac OS X Hints
http://hints.macworld.com/article.php?story=20060921215801114