Well it looks like it could be fixed in some scripts, by resetting the player group and the pirate relations. But, upon save/reload, the engine will save those relations in a set of hidden group attributes that are used during the savestate and restorestate actions. In this case, the restorestate is reading in those hidden group attributes and they are wrong for that particular playergroup/piratecitizen relation. So I thought a better solution would be that if there is an error of that sort in the restorestate, to just go ahead and fix them within engine. So now, no script hunting/fixing is necessary, it will just correct itself during the load of that save.
Fix will be in next update.