just to check I just re flew it for you, I always launch at 100, no higher, 5 seconds interval, making sure the ships are well within the target circles, 3 out of 3 missions, both missiles head for lead ship, as its destroyed by the first missile, the 5 second interval gives the second one time to turn and hit the second ship.
that's the same result continually, but I always fly low, in missions right to the deck then popup to 50