You have two separate things going on. The Gold issue is because you are running the Coinage civic. It cuts off all Gold and Silver in your cities but gives you +1 gold (treasury) per city that would otherwise have Gold and +0.5 gold per city that would otherwise have Silver. So that is actually working as designed. The other resources is something that another modder will have to look into. I tried a recalculation with Ctrl-Shift-T and it did not change the results. I even tried adding a Stone resource plus Quarry plus Road with WorldBuilder and it still showed exporting one Stone, after another recalculation.