What kind of car and where-area wise- are these patches located? I am thinking the metal may be shrinking-expanding at different rates than the stock metal. Cold roll metal is supposed to have a "grain" to it and may be the problem. Thickness and tensile strength? I am not an expert by any means, I have been to a few classes by Winfield, and he has mentioned that these things can make a difference. Personally, I would think a skim coat and a few coats of primer would have hid this, but like I say, I am no expert.
"When I was younger, I could remember anything, whether it had happened or not." - Mark Twain