There are a couple of possibilities why this might have happened; the paint is soaking into the surface unevenly even with a primer or the paint was applied unevenly.
I have noticed that a lot of paints now days are thicker, stickier and harder to use. I would blame the paint!
Try applying another coat of paint. If the paint is too thick add a little water to help it flow onto the surface. This might make it easier to apply as well.