I don't know what causes it But I did paint a house with the same problem on the ceilings. Less on the walls. We oil primed the ceilings and used SW Pro-Mar 400 for the finish. I was back in the house to do some other work 6 months later and it still looked great.If it's not thermal bridging. Could it be that the studs are holding enough moisture in them to keep that area of drywall and paint from drying out and fading as much as the drywall and paint that isn't over a stud?
What brand of primer and paint was used? Is the paint flat or does it have a sheen?
I wonder if an oil based stain blocking primer would solve it?