The only thing i changed in it was its name and adding it to the escort list.
edit: I tried to go around the problem by having them attack the Zephyrus and make its weapons and engines break down when its below 50% (afterwards an event is in place ordering them to ignore the Zephyrus but thats supose to triger only AFTER its disarmed and disabled). The only things ticked in its misc properties are Cago known and escort ship. The other pirate wings are set to ignore it but that cant affect the bombers can it? What gives?!

Update: This is realy wierd. when i removed the ignore command from the other wings the bombers worked fine. Of course now i have to find a way to stop the other fighters from ripping the zephyrus apart. Also the protect ship misc doesnt work. I thought that if i use that the bombers (who are ordered directly to attack the ship) would do their thing while the rest would ignore it, but it seems protect or not its still fair game to the other fighters. And if i give the ignore order to every other wing except the bombers via an event the bombers act asif they got it too. So on 1 hand the main target is untouchable and on the other it gets ripped apart before the capture ship even arives.