Sounds like what you need to do is to remove both ports and re-bed them. That is the proper way to fix the issue.
Whatever you do, don't smear silicone around anything. It won't fix it for long, and it will cause you a world of problems later, as nothing (including more silicone) will stick in that spot again.
On opening ports with a frame around them, I should think that smearing anything outside would be a temporary stop-gap measure at best.
I have fixed windows on my boat, and it had a small drip in the rain. I do not feel like removing and replacing the window while the boat is in the water, and I don't feel like pulling the boat for a weekend do to a proper repair, so I ran a small amount of latex exterior caulk along the top of the window (it is installed on the side of the cabin top, and sits proud of the surface.) So far, it has stopped the drip, and I'm hoping it will last until fall haul-out, at which time I'll replace both windows. Then, I'll have no leaks whatsoever, and I'll get rid of that little bit of crazing too!
Hunter 26s were built 94-97. Based on that age, it's certainly possible you'll need to start rebedding things... Here is MaineSail's article on how to re-bed with butyl tape:
http://forums.oday.sailboatowners.com/showthread.php?t=117172
For fixed windows, the recommendation is to use a purpose made double sticky foam tape to hold the window in place, then caulk with Dow Corning 795 silicone. I know, I said no silicone, but that's what seems to be industry standard. Some folks have used just the 795 and no sticky foam tape with good results. My windows have screws through them, but it seems they are not needed based on other's results with re-installation...
Brian
