Staining and painting wood on both sides to last a long time is a great idea.
However as you install each piece of wood you need to seal the ends of the boards when you cut them to fit. If you did not protect these ends the water will wick into the wood.. just as when the tree grows this is the direction of the sap flow. Then the moisture needs to get out and picks the sunniest spot that is trying to draw out the moisture.....wala...peeling paint.
Caulking the joints is a poor remedy which only makes it harder to fix once it needs resealing.
So try to seal every cut you make, which I realize is time consuming but very good for the long run.