I think the reason Dread Pirate
didn't put the Cathedral and Palace goals in the game is because once goals are reached, the game ends, and Dread Pirate liked endless games. He liked building huge populations.
So, I am happy to report that the game now works for me, too.
I am curious which pirate settlements were broken. I see there are three or four on the big island with only a Kontor and Towers.