Drive around for awhile and get the motor hot, then go home and spray water on the header leading to the cylinder. If its hot and the water vaporizes then its firing just fine and its in your computer. If it is hot i wouldn't worry about it. If its not hot I would do a compression test on that cylinder and see whats going on.
Do you know what else causes misfires? Plugged fuel filters and low fuel pressure. When was the last time that you replaced the AC-Delco Ignition wires which are good for only 50,000 miles before gaining too much electrical resistance and shorting out.
You may have a vacuum leak at that cylinder or an EGR system clogging and could just need the PCM reprogrammed.
I have a reoccurring cylinder 3 misfire on a 3800 Series 3 V6 Engine (non turbo charged). I have changed the spark plugs, wires, coil pack, and the ICM already and the misfire continues to happen. I've swapped the coil pack positions and the misfire remains with cylinder 3 so I know it is not a faulty coil pack right out of the box. I also changed the fuel injector for that cylinder with no change. Also swapped injector positions and the problem remains on cylinder 3. The engine runs perfectly fine whether idling, slow, regular traffic or hammering on it. It does have 200,000 miles on it though. I had replaced the head gaskets a while back because one had went bad and caused that famous super mosquito sprayer effect with the white smoke (LOL). The cylinder 3 misfire was present prior to doing the head gasket work so it is not something I've done on accident that would be causing this. The engine was stalling out sporadically for a period of time and that was fixed by cleaning the throttle body. It was sticking because it was gummed up in there pretty badly.
Has anyone else ever ran into this problem with a cylinder misfire that cannot be cleared and have you been able to resolve it? It doesn't necessarily have to be this exact issue, on the same cylinder, only the same symptom of a reoccurring cylinder misfire that cannot be cleared.
