Took my car to a shop today to get the battery replaced. He used an Exide battery which is what is stamped on a bmw battery. After he did this, he used his scanner tools to reset all the codes in the ECU, about 10 of them were electrical codes relating to the low voltage of the last battery. When he did that, he tried to log into the portion of the system to pair the new battery, but every time it was telling him that it could not connect(in BMW wording of course).

Not really sure what to do now. I drove the car for about 3 miles and parked it for an hour, when I got back in it, the clock was reset, which means the battery went dead again. Hoping that I just didnt drive it long enough to charge the new battery, even though the scanner was showing 14.2 volts when I left.

I guess my question is, do you think the PCM on top of the battery is gone bad? Or maybe his tools?(it was a po-dunk shop) or.......?

IIRC you should put in a battery that is 80% charged and that's the number BMW assumes when you register the battery. Double check the %, as I can not guarantee you that it is 100% correct. When I bought a battery at a BMW dealership they said it way ready to be installed (when I checked, my charger showed the charge around high 70s).

It's always much better to test a battery under the load, rather than simply with a multimeter.

Regarding the registering... What software is he using?