I upgraded the firmware in my Nav system - it's a Cooper S, so has a MK III BMW system.
Old rev version
First displayed after boot
Then you get a black screen for a bit - but don't worry... this will appear:
BUT if you click OK to reboot, but forget to remove the firmware CD and it gets sucked back in (whoops - I would never do that myself!! *rollseyes* ) then don't worry, just let it go. The following screen quickly comes up and you get to remove the CD and reboot again.