I've had this problem intermittently for well over a year. Had it checked by an independent and by the dealer on two separate occasions when it was lit but neither could find a cause and just reset the light. Sometimes I get it if I fill the tank with other than Top Tier gas. I put a bottle of injector cleaner in the tank and make sure I only use Top Tier gas and within a couple of tanks the Service Engine Soon light with the "Increased Emissions" warning goes out. That's not to say that there isn't really an underlying cause in your case.
There area number of other intermittent problems I have had with this car. The latest was the SOS Malfunction warning. That went away over night. Same with the 'mute' function stuck in 'mute' mode. I think there was one other but I don't recall what it was. It seems the car has the ability to "heal itself" if left to go to sleep.
2005 545i, Jet Black, Black Leather, Cold Weather pkg, Logic7, 6 disk changer, Sport Package, Automatic, moonroof, electric rear sun shade, dark wood trim, PDC, Xenon Adaptive lights, Nav, Sat radio, 245/40 ZR18 - 275/35 ZR18 tires, Progman 30.02