I also have this problem with my track bike. It's a 52cm, but the headtube is still only about 4 inches long (if that). I figure I'm going to try re-cutting a stem so that the quill portion is shorter, but only once I've found another usable dumpster-stem that I can butcher so as not to put a better stem at risk of saw-induced death. I haven't run into any stems that come that short from the factory, unfortunately.