If there is no power on the yellow wire but there is power on the orange one, the mk2 will run and it cannot tell that there is no power on the yellow wire (permanent feed).
This is being addressed with a slight change to the main board for the next 1000 units - don't panic, there's no extra functionality just a design cleanup :)
If the unit is powering off suddenly when accessory goes away (and +12v permanent fuse is ok) then the problem does sound like the "permanent" 12v supply isn't very permanent.
Hugo