I have had a similar situation.
Except I have a couple external firewire drives. The firewire drives are always wanting to go to sleep and they have to start up before the ipod will dismount. Sometimes one of the drives dosen't want to spin up again or something like that. Anyhow, the ipod occasionally remains on the destop even though the little ipod screen returns to it's little menu thing.
I just do a relauch of the desktop and everything is ok.
I don't know if this is anywhere near what you are experiencing.