Paint changes color when applied to Stucco. Chemical rxn assumed, but what?
You haven't told us the color of the stucco you are painting, nor the type of paint.  Chemical reaction is very unlikely, paint that changes color would make for bad paint.  Pigments are chosen to be stable.  Old stucco would be only a little alkaline, but it is porous.  This sounds more like color leaching out of the stucco and into the new paint.  You need paint with better coverage (covers contrasting colors) or better sealing ability.  Seriously, don't ask us, talk to your paint supplier at a paint store.  Maybe get them to refer you to their in-house experts.  You probably will have to spend more for the paint than you are planning on.