When loading up a savegame I noticed that ships that had been set to automanage their special abilities had switched back to manual. It appears that it is either not being saved or not being loaded and they are just using the default behavior - in this case manual.

Just to clarify, when I say "automanage special abilties," I mean automatically select new special abilities when they level up.

This is frustrating because in the late game you can have dozens of cap ships and trying to track them all down again reset their status is pretty painstaking. And on a side note, I wish that there was a way to globally tell them all to manage their special abilities (and if there already is a way please tell me).