+1 to post #3. I suspect your liner is going below dewpoint. Check the temp in your boat, might have to turn the heater up a notch.
I keep my boat in your general neighborhood, it has been a rough winter, cold and wet.
My harbormaster estimated he blew down the waterlines here 15 times this winter!
Beyond that, I suggest a product called "Moldex" because it kills the hyphae (roots) that are growing into your vinyl, which most other treatments can't do. if you don't kill the mold's roots, the stuff will just grow back. It is the only product I've used that works. I use it on Mexican mold after my winter place gets hit by hurricane flood and am happy with the results.
The scary part is what does the other side of the vinyl look like? I pulled one overhead panel this week in my boat and had to deal with the same issue you are working on.
I find it at big box stores or big hardware stores.
Follow directions, use eye protection if applying overhead. Costs nothing to lay down plastic sheet on your good stuff too.