As I remember it, the bi-color light fixture is on the foredeck of the 16.
Based on your symptoms, I'll make a guess:
1) There was a slight leak for some reason.
2) It has now wetted some of the deck core around the fixture.
3) So now it's not possible to get a good seal (because the deck is no longer rigid to compression there).
4) And silicone is not a very good bedding compound anyway.
I may be completely wrong, since I can't even see it - hence just a guess.
What I would do:
1) Remove fixture completely and poke around to see what you have.
2a) If core is dry, dig enough out to fill surrounding area with thickened epoxy (this will protect the core, plus give you a solid surface to fasten to).
2b) If the core is wet, dig out as much as you need to to get to dry material, and then proceed (method somewhat dependent on how bad it was).
3) Clean off the silicone as well as you can (it leaves a contaminant that is very hard to remove and keeps things from sticking, so check by seeing if water beads on the surface - if so, keep cleaning/scraping).
4) Re-bed the fixture with butyl, polyurethane, polyether, or polysulfide.
A last note is that if the fixture was fastened into the deck with "pointy screws," well, that never really gives me a happy feeling. It does work, but...
At minimum I would put pointy screws back but into epoxy. But what I usually prefer to do is one of two things:
i) Fill with solid thickened epoxy and tap for a machine screw
or
ii) If you don't mind nuts on the underside, drill through the new epoxy and use a machine screw and nut to fasten.
Again, this is just my thoughts without seeing it, but based on working on other boats.
Sunbeam
PS: I just re-read and noticed where you said you caulked on top of/next to the fixture base. That never really works in my experience. I see lots of people doing (and recommending) it, so I don't blame anyone who thinks that's the way to go (I've even seen it in "how to" videos). But it's generally either a temporary fix or not even a fix at all. Better to remove fixture, clean surfaces, and "bed" (i.e. caulk) under the flange (there is usually a flange of some sort). Then you clean around it after you are done so 99% of the compound is invisibly under the flange (i.e. no big "bead" around the outside, which doesn't usually do much except get dirty). So, there is the chance that the fixture just needs a proper re-bedding (but I'd do the core treatment while in there anyway).