Hey there fourrays,
The best thing to do would be to do a water test from the outside using a water hose to see how the portlight is leaking. It may be leaking at the actual seal around the inside of the glass, but it may also be leaking around the frame itself, past the sealant on the outside that would be under the frame that you see on there. If the window leaks past the outer frame, you will need to remove it by removing the screws, pulling the frame, and then scraping any sealant off the outside. Once that's done you can seal it with any silicone sealant such as 3M 4200 (do not use anything as strong as 5200, as that will be almost impossible to get off in the future)
If it's the inner seal at the inside of the flip down, then you would need to check with HMG HiTide to see if they can provide a replacement seal. The portlight is part number 593-315-05-02-02-1.750. Hope this helps.
Cheers!
Ralf
