As the original poster of this topic I would like to update the forum on the subsequent saga of our boat roof....
The initial blistered paintwork was completely removed in October 2010, taken back to the metal and then re-painted with six coats of primer, undercoat and topcoat...this was done indoors and boat out of the water..within 2 weeks the paint re-blistered, but not micro blisters, it blistered like the ones you get on your heels from a bad pair of fitting boots...the painter was unhelpful in the extreme and never put the problem right, but that's another story...
I subsequently discovered the process had involved 'panel wipes' that are normally found in the car industry, now I am no paint guru or scientist...but did wonder if that was the cause, if you burst one of the blisters it emitted an acetic acid smell...
Now thoroughly pissed off with 'professional' boat painters I took the stance of if you want a job doing right, do it yourself.... so I removed the offending paintwork, de-greased with white spirit from B & Q, and painted the roof myself using a well known brand of exterior metal paint (no not Hammerite), I did it outdoors, got the odd fly stuck, but they do break off at the ankles when paint is dry...and did it as scientifically as reading the instructions on the tin...total cost was £300..this was done in May, it still looks excellent...although I am blowing my own trumpet, it has now lasted far longer than both the pro jobs it has previously had...