I've had intermittent problems with this, too. I needed an oil change and had my indy check it out. They couldn't find anything wrong and reset it - no charge. Another time the Service Engine Light had come on I had to take it to the dealer for one of the recalls. I had them check it out and they couldn't find anything wrong either so they, too, just reset it - at a cost of over $100! I have had that light and the "Increased emissions" light come on and eventually go away of its own.
More recently, I got in the car, started it up and get the Service Engine Soon light and the "Engine Malfunction" warning. My indy checked it out and it was misfiring as the cylinder one coil was "shot'. They replaced that and all of my spark plugs and $500 later the car is running great again. I don't know if the intermittent problems were early warning signs but when taken to both my indy and the dealer thay had found nothing to repair.
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