Small world Geoff...We had our present enclosure made at Ships Tailor and specified Gortex after our last bimini had to be re-done with Gortex after 2 years in the Bahamas with regular thread.
I have no idea what was used in terms of techniques but we used regular sunbrella and the present system has held up quite well with no leaks whatsoever for 3 years. Maybe the needle size on your last one was the problem. I think the fabric wicks in moisture a bit as if you press on it during a heavy rain from underneath, you get a wet spot, but that is not due to stitching or thread. We've had several bimini's/dodgers and enclosures built by ST over 22 years in Deltaville and have always found the work to be both excellent and expensive...but whenever we've had a minor problem, they have been quick to remedy it. I'd say talk to one of the guys there about your concerns and I'll bet the resulting job turns out fine.