So just for clarification:
I did not add any music from the linux box, I only added photos.
Following the Linux Sync (adding photos only, or at least I think that is all I did)
The iPod displayed Everything correctly.  I was able to see and play the 1000+ tunes, and all the images.
At that point the iPod was working correctly.
 
The next time I plugged the iPod into the windows box, it went into this auto sync mode, and started
to re-sync every single one of the songs in the iTunes library.
 
Unfortunately I am not sure if I feel comfortable attempting to reproduce the issue, because I don't want to go back through that experience again.
I may try it some weekend when I have plenty of spare time.
 
I am more currious if others have had a similar issue.
 

 
On Tue, Sep 14, 2010 at 1:51 AM, Christophe Fergeau <cfergeau@gmail.com> wrote:
Hi Bryce,

2010/9/14 Bryce Alcock <ba.lists@brycealcock.com>:
>
> Then I went back to my Windows box iTunes to load a couple of new songs and
> a chess game.
> At that point, ALL the previously loaded 1000+ songs were gone from the
> iPod,
> and iTunes reloaded all the previous tunes plus the new 10 or 12 that I just
> ripped from CD.

Is it iTunes that didn't display all the songs you had added from
linux, or just the iPod? There's probably a small difference between
the way gtkpod writes the iPod database and what iTunes expects, which
explains why it got upset and ignored your songs :-/

Christophe