The ships, from what I have seen, will often turn themselves so that they are perpendicular to the incoming missile before they fire. This is done automatically. It seems to help with guidance and the trajectory. If the ship doesn't, then you sometimes get shots that are slightly off. That's why I was asking if you had the game intentionally set to manual.
Interestingly enough, I play a similar scenario using the same weapons. My ships all seem to work perfectly. Of course, I haven't had enough time to play test yours and mine and compare them. That would help.
Another thing that I've noticed is that ships that are stock seem to function better than ships whose weaponry has been altered. I don't know if this makes any difference or not. I do know that changes to the database often create some weird occurrences that aren't initially apparent. The game will play one way using once database, and then updating the database (even one level---you are one database below the most current) can sometimes play a role. In fact, I've been trying to conduct tests on your scenario using both databases, and then mine doing the same thing. So, that's like four different testing platforms for evaluation.
This may be difficult for the devs to track down since it appears to work perfectly on some occasions, and differently on others. That's why including as much info as possible is always the best.
BTW, I place the SORENSEN in there to SEE what is being seen. That way I can determine if the ships aren't shooting because they can't track it, or if they aren't shooting for some other reason. The RIM 161s need something to be able to detect the missiles at a great distance. There are a couple of land-based ones that can do it as well. The RIM 161E has a range of about 1300+ miles, but if it depends on its own sensors, then it won't see the incoming missiles until they are too close. If they are too close, then they can't fire at all. That's why I place it there. If you don't need it in the scenario, then just remove it. But, while you are trying to test it, then it's nice to be able to have it so that you can SEE everything.