Update:
So I was using my old 20GB iPod (fourth gen - from the dark ages) in my Exige and it was having the issues of not shutting down and/or not starting up correctly. I even checked and made sure the software version was up to date.
On a hunch, I pulled out my iPod "Classic" (video iPod) and tried it (after updating software) and it actually works correctly with the iPod interface on the Alpine headunit. It seems to be more "aware" of the presence of the connector and the on / off signals sent by the Alpine.
So basically it looks like it is a problem with older iPods...darn...another reason to go treat yourself to a new iPod.
