If the stone walk way or whatever is brand new, i would bet that the problem is actually the light film of motar still left on the stone. I would power wash or hose end spray the surface and have another person scrubbing with soap and water to remove the film.
After this, and with time, you should have a nice looking stone. This is just like after grouting tile, the grout film has to be completely cleaned off and this does take time.
But, I do not know of any protectant that will adhere and stay on flagstone.