Clutch in, give it a little blip and try again. This behavior is completely normal, although its severity seems pretty random. Sometimes I only get a little chugging, sometimes a lot.
By the way, this is not an M3-only thing. My 6MT 335i did it as well...owned that car for 4 years and I never understood why it did this. Kinda felt better about it when the M did it too
