Ag,
Are the tiles "slate" or "quarry"? you need to indentify what they are before attempting to clean!
Look around the internet first for pictures of various tiles to identify, or contact a masonary trade association for more advice on how to clean properly.
Slate tiles marks (when not sealed) will temporarily dissapear when wiped with water or other wet solution, (they change colour slightly), but when the surface has dried, the hue of the plaster mixed with water will re-appear from deep into the tile as the tile still has moisture in them.
In my opinion, you need to withdraw this moisture by using "silca gel " pellets , basically its the same stuff they use in babies nappys, or to withdraw moisture from caravans or boats etc.
Apply the silca and leave for a few days, and cover tile with a bowl and seal the edges of the bowl with tape or silcone sealer to stop more water ingress, after a few days remove bowl and then vacuum up the expanded silica, finishing of with a stiff dry bristle brush, and vacuum again, do not use water, then you can decide to leave them natural or use a relevent tile sealer.
Do test first on a inconspicuos tile, to see if there is any reaction to the silca.
hope this helps, let us know how you get on!