The op says that he has resource bases of wood, stone and iron.
I will ask the other obvious question in that do you have the capacity (storage) to receive the resources from the boat?
Edit If you determine you should be getting more than gold from your resource boat then I would encourage you to contact the game support. They are in the best position to advise you as this should not be happening. They can also see if others are similarly affected. Let us know if you get it fixed and how please, so if others are affected then they have the info.