I had water leaking through from my cockpit into my back hatch in my Tahsis. Since it had originally been sealed with silicone, I went with the marine silicone. It worked like a charm and lasted a good couple of years. The issue is that once silicone has been used, nothing else will adhere to the surface, so if you use silicone that is all you can use in the future. I think the putty you are referring to might be the epoxy putty mentioned in earlier posts. I filled in some damage made by a rock on my skeg box with same, and it is still in good after a couple of years.