I thought that I'd read that the carboned up areas have fuel in them and the clean areas lack fuel. Maybe it is along the lines of what Chevy TS talks about with the wet flow, maybe the atomization isn't good or there isn't much swirl going on to move the fuel all around inside?

What heads are you using and can you see swirl patterns in the chamber? If it would be a fuel wash as Andy suggests, I would think you could see that in the chamber better than on the piston top.