I think it all just comes down to the fact that the misfire code is to sensitive, all engines misfire when cold. Its just the nature of the beast, thats why the cars run rich when first started to keep that to a minimum. For whatever reason the ECU starts looking for the misfire code to early while the engine is still cold. In the software I use for GM trucks you can tell the ECM when to start looking for misfires, by pushing this out to almost operating temp you can get that pesky code out of the way.
Its more or less just an emissions code, I mean to many misfires would wreck havoc on your cats. But if it gets to that point you will most definitely be able to hear it misfire.
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