This gets interesting, which means it gets frustrating.
OK, It turns out I did eject the unit correctly. There is an eject button. First the Ipod said to wait, then it said it was safe to disconnect.
After that, I couldn't use it as a portable player, because the Ipod said it doesn't have any songs. But it does. If I plug it back into Amarok, they're all still on there!
If I plug the Ipod back into a MS Windows computer, ITunes says it can't read the device.
I've been able to use Amarok to move my music library onto the Linux computer though, so that's interesting.
Any help is appreciated, thanks,