Have you tried changing the diff fluid? Some diffs will make noise IF the person who broke in the drove the car faster than 170 kph (and HARD!) during the break in period.
I would change your diff fluid and use the special BMW diff fluid with "+FM" (friction modifier, booster). Castrol SAF-XJ +FM
, bmw part #83 22 2 282 583 SAE 75W-140
SAF-XJ + FM BOOSTER
Castrol SAF-XJ + FM BOOSTER
, bmw part #83 22 2 282 583
regular Castrol SAF-XJ diff fluid...
(sold thru out Europe and BMW Zentrums over here)
BMW NA uses this +FM diff fluid to quiet diff noises at low speeds. But its mostly for low turning speeds. Like say for a U-turn or when parking. Still... changing your diff fluid won't hurt anything. You should have it changed every 45K miles or third oil change.
I do not believe that the +FM fluid is used in Europe. Only for us cranky and complaining US guys! lol So I would special order some and see IF it gets rid of your diff noise.
CORRECT 1M Fluids List [Engine, Transmission, Differential
The other thing you might want to do is change your transmission fluid. I don't buy into BMW's lifetime fluids.
I am not sure about the DCT trans(code) that the M3 uses, but I bet these guys would know which ZF trans fluid you should use. They also sell filter changing kits and have some good ZF documents on their site.
CTSC... ZF Lifeguard fluids....
Sounds like having your car's SW(software) update has fixed 90% of your woes.