Sounds like you had a clamping drain installed with a liner. Out of curiosity, is the liner flat on the floor, or is it on a sloped preslope? Normally, the top part of the drain is adjustable, at least a little. BTW, if the liner is not sloped, the water that gets below the stone will accumulate - it may promote mold and smells in the long run.
The best place I've found for questions on tiled (or in your case stone) showers is www.johnbridge.com.
How thick is the mudbed by the drain? NOt sure the best approach, but you'll get some comments from professional tilers where indicated.