Any pictures of the offending bubbles ? That might help identify what you're dealing with, if it's actual air pockets in the gel coat (which isn't common but does happen) or the results of a paint reaction.
Bubbles in the gel coat can occur with hand layup and if they are fractionally sub surface they can cause problems with temperature changes. We occasionally had this problem with fibreglass vessels on chemical duty at elevated temperatures, they'd look fine at the start and then after a period of service you'd see "holes" on the inside, the trick being to determine if this was fabrication or chemical attack. Normally on a car body it's not a big deal but whenever I've done a respray I've tended to press a screwdriver on any suspect areas and fill any that collapse. I think a similar procedure was followed by Lotus and certainly TVR in the 70s.
Another thing I've seen is reaction between paint layers, not whilst painting but several years later. When we moved here the outbuilding roof was leaking where I stored the Europa and I covered it with plastic sheeting - for several years as it turned out
Anyway when I finally dragged it out there were some bubbles in the paintwork. I stripped off the colour coat and then found the surface beneath was "speckled" with hundreds of white circles about 1-2mm. Very weird, but I guessed it was water vapour trapped between the paint coats and caused by my poor storage. It wasn't in the gel coat and stripping to bare fibreglass solved it.
Brian
