I resealed mine last fall (95 Islander). I removed the aluminum frames from the deck and took them to a glass shop to have the glass re-siliconed into the frame for like $10 each. I took the time to clean all the old sealant off the glass and frames. Use acetone to clean them. The frames are bent to fit the deck and the glass is flat. The problem is also with sealing the aluminum frames to the deck. Many of the screws do not pass through the fiberglass but simply slide by the fiberglass edges. (poor QC when cutting the opening) I used lots of 100% silicone when reinstalling the aluminum frames to the deck. Also silicone the screws in place. put silicone on the screws and under the head prior to turing them in tight. You should also reshape the inside aluminum cover trim so the screws can tighten into the grooves. Allow the silicone to dry over night, then carefully cut away the excess with a razor. It may take a few days to get the frames back and installed, I covered the openings with plastic sheeting and painters tape in case of rain. Check the seal prior to replacing the rubber cover strips to check for leaks. The rubber strips ar not used to seal the windows.
I also had leaking from the horn wire pass through as well. I had to remove and reseal this as well.