Had the same issue in 1.05 - had to turn it off as well.
I hope the fix that Blair mentioned will also address the issue of repair bays not targetting damaged cap ships within range automatically. A number of times early in a game I have limped my egg back to a planet with repair bays and parked it within repair range and the repair turrets haven't done anything. I have to get them to work manually (select all, press tab and Q and click, tab, Q and click etc.... Pain in the backside when I want the ship repaired to send it back to where the fight is as I have to baby sit the repairing, rather then micro the fleet battle. I normally get into this situation after killing the enemy Progenator and then running from his illums as opponent trys to return the favour. If I pull it off, he is in trouble as my next move is to jump back and nanite his factory and pump phase missiles into it:)
