I wasn't aware of that that you did not use the turret skill on missiles. I only have the rules as they are presented in fantasygrounds, so I must have missed that detail someplace.
I used stock ship that came with one of the books. But I noticed now that when I added a ship from the spacecraft tab the armor was not listed in the defense section on the combat tracker until after I had opened the starship info in a seperate window and then clicked the systems tab.

