Photos would help a lot. The problem will be sealing the aluminium to timber well enough to stand the test of full seasonal changes in an exposed situation, and one little leak that you don't know about the timber will degrade over the years. Is there anyway the timber itself could be chamfered enough through planing and sanding to create a fall? Since water is getting inside it also sounds like the flashing has failed (or was installed incorrectly, or not at all). Again, photos will help.