I had the same issues, and the first SA I spoke with said I had to replace the battery. $$$.
The next advisor gave far better advice. I don't know if this part is true, but he said the "charging" system in M3s (and presumably other BMWs) is more of a "maintaining" system, and that it can keep up with the car's electrical demands, but not really add a significant charge to the system at the same time.
His advice was to buy a charger, and not a trickle charger. I went to Canadian Tire and bought a "smart" charger, that switches between charging and trickle charging based on the the current state of the battery. It was about $90.00 regular, on special for $70. I gave it an over night blast with it, and watched as the amperes going into the battery went from 3.5 down to 0.5, to zero.
I haven't had the problem since, and the battery is now 1.5 years older than when the first SA told me it had to be replaced. No more warnings, and I can again be less careful about using the "rest mode" on the climate control when I'm parked, and using all the gadgets recklessly.
I'm sure there are other chargers that do the same thing, but I couldn't be happier with the cheesy Canadian Tire unit.