Atrocities:
I hope you will try going through the system again and trying to make it work for you. One thing that may be causing the ship design bug you're describing is if you're using a different Version of SE4, or possibly even a modded Version.
I know the TDM mod is compatible--it only changes the AI--but other mods that change components, etc, might cause your turns to be played by the AI. Just a suggestion.
LL (AKA Eric the UI Guy)
http://seiv.pbw.cc/