either you stripped the s2k antenna, or like you said, the s2k antenna has a shorter thread- just push down a lil when screwing in. i also recommend putting lock tite on the threads to prevent theft (blue bottle for car use). and like dan said, you dont need to take out your antenna when going to the dealer. in fact , i wouldnt take anything out when goin to the dealer for service, just take the mods like Intake
, pulley, etc off when doin warranty work.
hope this helps