Ok I got to the bottom of it.

Actually Bob Hauck's post got me thinking and what happened was that I
originally had auto-sync (within each program) turned off, but when i
played with Amarok and switched to MySQL I did a re-install and of course I
forgot to set it off again.

Bottom line, if I did the same thing under Windows with say MediaMonkey, it
would have done the same thing.

The only complaint I have is that MediaMonkey does ask for a confirmation
and warns you that another library exists.

Bottom line, don't sync an iPod to two different programs, even under the
same OS even if both programs point to the same location for the local
files.

So Linux is off the hook and I get to eat crow, again...

--
Moshe Goldfarb
Collector of soaps from around the globe.
Please visit The Hall of Linux Idiots:
http://linuxidiots.blogspot.com/
Please Visit www.linsux.org