Connected the battery I'd been using jump leads from directly to the car (i.e. removed flat battery completely and attached spare direct to car).... Fired straight up

Given the behaviour I'm guessing that for some reason the factory immobiliser doesn't like anything attached to the fitted battery if it's flat.... I'd appreciate any inspired thoughts that would clarify what was happening, would hate to be stranded somewhere and not being able to start the car even with a powerful jump pack.