Sounds like a possible dribbling injector, Get them checked out. I.E when on atmospheric running it is running too rich hence the miss-fire, then when on boost it clears up due to the volume of air being forced into the cylinders. Also you didnt state what injectors you are running. If you are using injectors that are to big for your engine setup then you can run the risk of bore wash which will leed to a costly rebuild.