I'm assuming the paint you used isn't the same paint used 3 years ago, but recently purchased (same color). Unfortunately, there are variations of color and sheen between gallons of paint (of the same color) and these differences are more dramatic from old paint to new paint.
I hate to be the bearer of bad news but you will have to repaint your ceilings or live with the blotches. If you repaint, make sure you have a full gallon left over for touch-ups. Always intermix your paint before application.