I doubt it is an ECU problem Phil, it is usually all or nothing with that, or running very bad. You are back to checking the usual things, plugs, leads, screw plug caps are tight, fuel pressure and ProTune 2 for fault codes and Lambda sensor operation. Not experienced a CPS fault but I would expect more problems than an occasional misfire. A bottle of injector cleaner through the fuel system never hurts. If you have another M3W available you could transpose the ECU just to eliminate or confirm your suspicions? Is the misfire always on one sides cylinder? The RH cylinders often seem to run a bit "fluffy" at idle compared to the LH if you feel the exhaust.
