Had a persistent leak with my cabin hatch the was coming from the window seal. No matter what I did, the leak returned.
Was able to solve the problem by purchasing a new BOMAR low profile seal from west marine.
Removed the top half of the hatch at the hinge.
Cut the caulk and pulled out the window from the frame. (cover the opening with a sheet of plywood with a weight on top to keep out the critters)
Cleaned the frame and glass of all the old butyl tape and black glazing caulk using a plastic scraper, rags and acetone.
Re-seated the window with double butyl tape to hold the glass to the frame, taped the caulk lines and sealed with GE black silicone glazing caulk.
Let the caulk cure overnight and reinstall.
The leak is gone.