I did as the manual says and have had no problems now at 3200 miles. At almost a .5mph or just before stoping I have heard a little squeak but nothing big to worry about. I have a '04 Saab 93 Aero and after a while, the original brakes at about 49,000 mile now squeak but I noticed that my driving technique is a bit different with the M3, on the Saab I brake softer/longer and with the M3, shorter and harder as if not worring about break wear. The Saab tech once told me, every once in a while romp on the brakes a few good times from higher speeds just like bedding them and it does work. He had mentioned that the brakes/disc get a bit glazed from normal brake use.
I did the run-in step down from about 70-20mph several times and let them cool, then do it again and have had no problem on the M3, but not sure if that was the proper method. I waited after the 300 mile run-in as the manual specifiys first though.