After the re-run, instead of just one Hydra baseship dissapearing... I lost additionally another ship. I got the "Built ship" message for both, but the ship is not there.
I'm afraid that whatever is happening is not fixed yet.
One comment; I just realized that the PLS should be sending at least a message indicating whether it is active or not. I am not receiving any message, so it may not be working. The Zeus is not working either. This might give you a clue on what could be happening.