The pure gold PPG base isn't a heavy flake, I've used it before and it's just a basic gold basecoat, so any flakes even if they were standing on edge would easily be buried after two or three coats of the wine. Maybe you got some dirt specs when painting the gold which are now high spots that are being knocked off when you colorsand the clear? Are these spots consistant in size and shape? round? sharp? Also it could be some wrinkling of an undercoat like previously mentioned. A picture would sure shed some light on the problem.
The sad news is there's really nothing you can do short of doing the whole thing over. 3-stage/candy paint jobs are nothing the amature should tackle--many professional painters have problems getting these products on evenly. If someone wants a candy job done I usually try my best to try and talk them out of it, eventually the car will be scratched or chipped at some point down the road and repairing this stuff is usually a real challenge. Save the candy jobs for show only vehicles IMO.