Inspectors have an issue with clipped headed gun nails because they can be over driven causing a decrease in holding strength. If they aren't over driven into the wood, they have the same holding strength as full round headed nails. Don't let the inspectors walk all over you. Make nice nice to a point, but don't let them take advantage of you just for ease of passing their inspection. I know Senco provides engineering specs for their nails should you butt heads with your inspector.
Just want to add this note. If full round headed nails aren't fully driven into contact with the wood, you'll have the same holding strength issue (under driven).