deck leaks
James,to answer your question ,yes ,the horizontal windows will leak as well as the hatch.If it is the windows they most likely will leak inside the boat not the liner and should be pretty easy to see so should the hatch as thet are both sealed and should not (notice I said should) leak inside the liner.I don't know if you sealed the compression post where it sits on the cabin top might want to check there.Maybe remove the cover plate around the compression post and some of the lights and have someone spray a hose on the boat to see where the "leak" is.Another posibility is to rebed the screws on the cover(sea hood)above the cabin top where the lines run thru.Also check the dorade vents for possible leaks.Sorry not more help but you can rule the windows out as a source because if you had one out you would see it is cut out and glased over so that it is sealed except for the screw holes that should be caulked over.At any rate good luck and keep us updated when you find where it leak is!