I was having that problem too, I noticed if I go into the dedicated server via in game "dedicated server" or "host server" my admin credentials would work. I also noticed that I had an additional server folder in C:\Users\James\AppData\Roaming\Avorion\galaxies, make sure you're using the right one! Most importantly, what I was doing wrong, is you must execute server.bat, then launcher.bat, I was only launching launcher.bat at first, which would still start the server, and allow me to connect, but I had no admin functions.
Here is what the inside of my server.bat file looks like:
bin\AvorionServer.exe --galaxy-name Galaxy of Terror --admin 123456789101112113_admin
--use steam-networking 1
--collision-damage 0
Steam64 ID is made up and an example only.