Your problem reads like the egosoft own behavior of carriers under attack, they deploy its armed ships. To prevent that behavior, there is a own setting in the "Code of Conduct":
It automatically disarms docked fighters (weapons get uninstalled but stay in the cargobay of the fighter) when they dock and automatically rearms them when they get started.CODEA Manual wrote:Automatic disarming in the hangar
This function allows to automatically disarm fighters of the different branches while they are docked. This prevents that the ship's own defense system starts the fighters without control by CODEA.
calmterror:
Listens to me, as your script files got corrupt somehow. I suggest to re-install the library/codea script files. If these files are not up to date, you may install a recent version of these files too, especially for the library.