It'S not you i have comfirmed and sent over to IC replays and details on the starbase not firering at 3 targets when the base is actively targetign a cap ship. Teh way to go aroudn this is to give a target quest order tot eh startbase that has no cap ships in it that way it will continue to hit 3 targets per bank.
I havent been trying to work out and see if capship suffer from the same problem starbases but have not been able to clearly spot it yet. Would need to get into a better control inviroment fight. Thinking fo creating a small senario with forge tools. But since the codeing for banks on caps and base must surely be the same it would be a very safe bet that caps suffer from this problem as well.