So I'm not 100% sure what the behavior currently is. I've got a point defense missile launcher, believe it or not, it works pretty well. However when you set a target, the launcher will point towards a fighter or incoming missile, fire, and the fired missile will go towards MY target, not the PDML's target. Weird thing though, because that doesn't happen 100% of the time.
Try it for yourself. when you're not targeting anything, or you're shooting it manually, everything works great.
Things only go sour when you set it on automatic, then set a target.
http://www.mediafire.com/?h00adn9j8yb1uov