Thanks guys.
I'm currently halfway through a "force total rebuild" using the librarian software.
Spin - you weren't wrong when you said it takes some time. It's been running for an hour and a half so far, and it's STILL only about two thirds of the way through!
I just hope it solves the problem. If so, I'll update the other ipods tomorrow.
Watch this space!
Edit: Ok...it took two and a half hours, but the librarian software finally finished rebuilding the library on my ipod..
I then crossed my fingers and plugged it into the D2, and success...the duplicate playlists have disappeared, so problem solved.
I'm off to bed in a minute, so I'll have to do the other ipods tomorrow.