It is usually a reaction between the metal and paint.
You used maybe different brands of paint but they were all emulsion based.
Emulsion paint is not designed to cover or act in a non reactive manner towards the metal pegs.
If the skim on the boards is really thin, the paint will leech into the skim and react with the pegs.
Grab some white gloss paint and paint one of the spots.
then give it a very light sand and paint it twice with the same paint you used orignally on the ceiling.
See how it looks.