Any idea how that happened? Did fresh water or extreme humidity get into the wood? What's the texture like? Is it solid or soft? Wet or dry? The reason I'm asking is to rule out rot.

Another good test is to tap on it with somethig hard, like a tack hammer and listen. If it sounds muffled instead of clear then at the very least the wood is too wet.

If it's solid then it's probably mold, not rot. I'd give it a soaking wash in denatured alcohol to try and kill any spores. let it dry out and then epoxy it.

If it's soft and punky, crumbly and/or sounds very mushy, it's time to replace the bulkhead.

In any case, I think that color will not be sanded away. In fact, if you've already sanded it a lot, that may be the glue line between the veneers starting to show. Paint is your friend.

Laszlo

Thanks Laszlo. I don't know how this happened. The basement has never flooded, and I've never noticed excessive humidity. For what it's worth, this affected the frames only. The panels don't exhibit this problem at all.

I sanded a little, and the appearance improved quite a bit, although there is still some discoloration. I will not sand further.

I tapped the frames, and the sound is sharp. The surface is hard.

What do you mean by a "soaking wash" in denatured alcohol? (I think you must mean something other than going over the frames with a rag soaked in alcohol.)

   If your discoloration is indeed mold or mildew, my recommendation is to wipe down with a strong bleach solution; maybe 10 to 20% ratio mixture of unscented laundry bleach in water (or about 1 cup per gallon).  Wear gloves, wipe everything down, use a fan to dry it out, or even better yet get the boat out in the sunshine.  Not only will this kill everything that might be growing, it also might help to remove any discoloration.  If you use a cotton washcloth or rag and don't rinse it out, it will start disintegrating a day or two later, so be advised to not splatter any good clothes you don't want spotted, and to rinse well any wiping rags you want saved.

I've never had to do this bleach treatment to any wood on a boat, but frequently done to old wooden or concrete patio decks as the first step in getting ready for a new stain job.  One day in the sun after a bleach treatment and almost all discoloration of the wood is gone.

While the mildew certainly could get started on clean wood, I'll mention that any type of organic contamination on the wood surface, when subsequently left in a humid/moist/undisturbed environment is when I most frequently have seen this happen.  For instance, an oil-treated/sweat soaked leather bike seat left in a cool moist shed for the winter - looked like it was growing moss in the spring.  Or the bottom portion of an old wooden dresser in the garage near where the dogs are fed - keeps wanting to get mildewy. So maybe you sweated on your frames? Or they were in the garage when you fired up the bucket of oil to fry the Thanksgiving turkey?

Adding to Bubblehead's recommendations if you're still confronted with stains that remain that you want to reduce before continuing, a long-time remedy for stains on wood is a water solution of oxalic acid applied then allowed to sit for ten or fifteen minutes then rinsed.

Another's plain, undiluted drugstore variety 3% hydrogen peroxide.

Further some also advocate neutralizing any acid left behind with a water solution of common baking soda but I've never found that necessary as long as a thorough rinsing with clean water's done once the bleaching effect has run its course.

DO NOT mix common household bleach with oxalic acid, or anything else for that matter. Bleach is a chlorine compound that liberates free chlorine gas when combined with most acids or organic matter. It's the chlorine that does the bleaching so you don't want it in contact with any part of your body.

So if a bleach bath gets you the desired result, you're done. If you're not happy after the bleach treatment rinse the wood well, let it dry then try the oxalic acid bleaching solution or hydrogen peroxide for further stain removal, then rinse once more. 

   Well, now I know.  I almost mentioned Oxalic axid in my first post, but then didn't because I'd never used it on wood, and worried there might be some negative impact.  Good to hear it can work on wood too.  I've found Oxalic acid to be probably the best and only thing that really works well to remove stubborn rust stains or waterline discoloration from fiberglass gelcoat.