The initial release of Anarkis Defense System 2.55 had an annoying bug preventing the docked ships from being set as inactive. Moreover trade commands ignored active/inactive settings, this is also corrected.
The version number hasn’t changed. So if you’ve downloaded ADS 2.55 recently and experiencing issues with active and inactive ships, please download again and overwrite previous files.
If the problem is still here, open the ADS manager and select “Uninstall”. Don’t do what the message tells you, though. Save and reload your game instead. It will reset ADS completely and fix the problem (you’ll have to re configure your carriers).