A photo might be helpful. Since moisture has been ruled out then most likely the staining is caused by the internal environment. Many things can react with paint and cause stains; air fresheners, candles/incense, cooking fumes, hair spray, dust, etc. All of these things settle on the various surfaces and react with the solvent in the primer or paint.
At this point your painter needs to seal up the stains with a stain blocking primer and repaint the affected areas. I would use an oil base or shellack primer to make sure the stains are well sealed.