I'm having the same exact issue with my iPod/sync and when I disconnect the iPod it plays all my songs from the one song that the sync was repeating til I hit shuffle on the iPod again. I checked the 3 iPods we have and the system does it to all of them.
Also from your story I am glad I avoided the MFT and the auto tranny which seems to be pretty problematic for a good percentage of owners.
'12 Focus Red Candy SE Sport 5 spd
'99 Toyota 4Runner Sport
'11 Subaru WRX STI Hatch