a short is one thing causing the trans program message but Did you also have the mechanical symptoms that Matty described?...Hope everything gets sorted matty with the least possible fu$$.
The symptoms matty described in his original post are, basically, while driving, the clunk he heard and felt, (I too felt it), was the car dropping down to either 3rd or 4th (not sure which gear it is in the 5speed auto) and then just driving in limp mode. As I am sure many people know, but for those that dont know, Limp mode is a feature BMW use to save any further damage to their trannys. Basically, your car matty, which feels like it is slipping, is actually attempting to take off in 4th (or 3rd). One or the other. Anyway, thats why, I would again be looking at either a) the wiring loom , or b) getting another opinion from another shop, and have them hook up their computer to tell them what your problem actually is. Anyway. Bedtime for me. Cheers for now Matty. Lost in the mexican state. cya.