It was apparent because there was no problem until the captain learned the jumpseater was an FFDO.
When there is a problem involving a federal officer on an airline flight it is investigated by the FBI.
As I said, If you really believe that captain's authority extends this far, refuse an FFDO the jumpseat and be honest with him/her as to why you are refusing the jumpseat and see what happens.
Regarding refusing the jumpseat for no particular reason.
If you have refused to carry others please provide details. If you have done so and have not heard anything it is very possible that the pilot involved simply chose not to report the incident to either his/her jumpseat committee or pro standards.