It sounds like your either your moving on to the next stone too quick, that's if your stroke is good. an uneven stroke can leave scratches. if thats the case your better dulling the edge and going back to the 1k to reset the bevel.

a 12k shouldn't leave any scratches or if there is, they're tiny scratches. See how it shaves and if it doesn't, you know you need to reset the bevel again.

good luck