Carrier command software bugs?

[NomiChirps]

I bought the Carrier Command Software for my Mobile Pirate Base TL just to try it out, but a few things about it seem broken. The "Should replace ships" and "Use shipyards to repair/replace" options can't be toggled, neither with arrow keys nor by clicking. And the TL itself now spams me every few seconds with the "Your ship has finished its job" log message, even when it's just sitting in empty space with no orders. I haven't tried the ship management features of it yet. Is this working as intended?