If the screen says that the pirates are dead, why there is another pirate base on the map?
Did you start with pirates set to inactive?
If you start with them active, and they have more than one base, they should not show as defeated (broken glass) until all bases are destroyed.
If you start with them inactive, they show as defeated and don't raid, but they do still have bases. Their bases are part of the map itself, and can't be added/taken out by toggling their active/inactive status.