cant say what precisely is causing it, but its just a bad mod / col file. i think that'd be it, not really any other reason that explains it.
if you get a 100% savegame, the hunter will appear in ocean beach, sort of near where you take missions for colonel cortez. it also appears in the army base near the airport all the time even if you dont have 100% (im pretty sure it does)
if you have played vice city stories, one spawn location is near where you go to do some missions for lance including "turn on tune in bug out" or whatever its called. the heli is right near there.