I had the same thing.  I think you actually get down to glass.  What I did, was just hit a spot that appeared to be fabric, with a light coat of varnish, with the theory that if it didn't go away, I could just sand off the varnish, and coat again. First coat of varnish, and gone.  What I do see though, in the sun when the sun is at a cetain angle to the boat, is refraction through the glass, and you can see the weave. Higher angle rays, and you can't see anything.  

In my experience, if the weave disappears when it is damp (with water), it will also disappear when coated with varnish.  I'd say varnish so you can hit the water! 

If you're really worried, you could hit the trouble spots with varnish and see if you're satisfied with the results. 

Paddle and ignore. It's all good

Varnish it. I can still see the weave on mine if I get the right light angle. The fabric just has different refractive qualitities and you will always be able to see it if you look at it right. But, casual observers don't see the weave and always remark to me how suprised they are that the boat is completely fiberglassed. Dave

probably more correct to say the weave has different reflective qualities and the coating affects the light refraction and whether or not you can see the weave. 

FWIW, here's my current analysis:

The rough surface of the thin sanded epoxy diffuses the incoming light around the glass fibers. The glass fibers being smooth exhibit only specular reflection, not diffuse reflection. Since they are lighted from all sides, anywhere you look you see the light reflecting off the glass so you get a white outline of the glass which ends up looking like a white weave pattern.

Where the epoxy layer is thick enough, the diffusion of the light happens far enough from the glass that there's not enough scattered light inside the epoxy to illuminate the glass, so no weave pattern.

Adding a layer of water, alcohol, varnish, epoxy, etc. fills in the surface roughness and thickens the layer over the glass, both of which act to subdue the reflections off the glass.

If you actually sand into the glass, you create a light pipe which channels the incoming light into the fibers, illuminating them no matter what you cover the exposed layer with (barring an opaque paint).

That's why if the weave pattern disappears when wet it'll disappear when varnished, but if still visible when wet it'll be visible under the varnish.

Because glass and epoxy/varnish have different refractive indices, there's always a chance for a light angle that makes the weave visible. The better the workmanship the less of a chance, but it's always there.

Laszlo

Thanks all for your thoughts and encouragement you really are a fantastic bunch to go to for a first timer like me! Today I sanded some more and started drilling holes for some of the fittings (which was terrifying). 

Laszlo I like your current thinking on this: it's all about diffusion and refraction. There were a couple of spots where I'm sure I did get into the glass, in those spots, instead of just being able to see the weave pattern, it was possible to see a prismatic rainbow effect as I moved around the spot. Coat and sand!

So exciting to be closing in on it!

When it comes to finish, I use a ten-foot rule: my boats all look fantastic from ten feet away. I would be less likely to use a boat with a furniture finish. -Wes

wes thanks...I should thank you, too, for your ganymede and other building blogs: back in October, they played a big part in helping me decide to go ahead with the Wood Ducks. I thought of you when I was purchasing my plywood at Boulter's in Somerville, and experienced, calm builders like you and Lazslo have really played a big part in my recognizing how much fun is to be had in the construction shop. I never would have guessed how much I would relish what so many must consider drudgery. Would love to hear more about your favorite paddling places/experiences around Cape Cod; once we get our ducks wet in some of the rivers around Boston, I'm sure we'll be venturing down there.