I have yet to find a way to absolutely remove the marks. Be sure you use different areas of the stone face to even out the wear. I have had decent success using the same 50% denatured alcohol solution I use with diamonds as well as a 'stone eraser' (rubber sanding belt cleaner), soft brass and stiff nylon brushes. Base cleaner helps as well, as I'm sure other cleaners along with some soft abrasives and elbow grease.
Had the same problem. I found that just putting the stone in water for a bit got rid of the large majority of the marks. I think you will have better success with the above suggestion from Alpinord though !