There's no easy way to fix it, or rather, to force the game do what is not supposed to. The game attempts to assign the closer enemy target area, but depending on the complexity of the terrain, such target area can even be beyond the mission radius of the helo's data.ini. Simply put, a terrain must provide target areas close to a given helicopter base, otherwise the issue remains; the values in the helo's data.ini are "disregarded" in the absence of close target areas to assign to it.
Strike Fighters was never designed to feature helos, so end-users must live with certain oddities when flying those.