It sounds like a possible injector/carbon issue. If you have a slightly leaking injector, that fuel will collect in the cylinder when the engine is off and cause that cylinder to miss when first started. You should also see some smoke due to it. Hook a fuel pressure gauge to the rail and see if it bleeds off after engine shutdown- if it does, pull the rail and inspect. Carbon buildup on the valves can also cause a similar problem. A good quality fuel system service should remove this buildup inside the engine.