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When boats are molded the gel coat is sprayed into a mold. For the boot stripe an area is masked off and after the hull color is sprayed in that masking is removed and the boot stripe colored gel coat is sprayed. There is overlap of the boot color over the hull color. Sometimes (used to be the norm) the whole is then sprayed with another color coat called a "veil coat". The purpose of the veil coat is multifold: it makes the hull more opaque so light doesn't show thru the otherwise translucent hull which is disconcerting to some; more importantly, when applying the first layer of fiberglass mat bubbles are more apparent and so corrected during layup. If those bubbles are not rolled out one ends up with unsupported gelcoat which soon breaks. Another reason is a color shift for the first layer of gelcoat; if white is backed with blue it looks brighter, if backed with grey the white is more muted.
Now to address the problem I think you are describing which my boat also has and is not that uncommon. There seems to be issues between the two or more coats of gelcoat. Often the small pox have a single cresent shaped crack around the pimple. If the blisters are just forming the crack may not yet be present. If one were to place a piece of adhesive tape with a fairly strong stickum on it like duct tape and really rub in on and then remove it like a bandage with a quick jerk, the top of the blister will often be attached to the tape. Looks bad and is a pain to deal with. However, if one looks at the bottom of the newly formed hole (bottom of the pox) you will see that second coat of gelcoat not raw glass laminate. That's why the tape test, so you don't have to worry that you have water in direct contact with unprotected fiberglass laminate. If you see the second layer of gelcoat the problem is cosmetic not structural. If you see fiberglass the issue may be more serious.
How to correct if the problem is cosmetic: It's not hard but is labor intensive, pop the blisters, then fair and overcoat with either a gelcoat or gelcoat type finish (Duratec 1040) or paint. Realize that they can form in other places on the hull and so figure that into whether or not you want to spring for a LP type coating.
Hope this helps,
As a disclaimer: I addressed this problem on my boat in the mid 80's with the assistance of the man who was in charge of creating the fiberglass animals (whales etc) for the Monteray Bay Aquarium. We used a gelcoat and additive (like The Duratec 1040 mentioned above). I still have that boat and yes, in unrepaired areas the blisters have returned. I've learned to live with them.