Looks kinda like this:
System boots from 3.1 ROMs on motherboard, then very early in the bootup it loads the ROM image that comes with BB 2, after which it reboots once more to run from the softkicked ROM.
I'm getting tired of hearing my WarpEngine chime twice on every power-up of my 3000T.. Where's a set of those 3.9 ROMs when you need one...