First, if the liner is flat on the floor without a preslope underneath it, it is not installed properly and you should start over! THen, multiple waterproofing layers is never a good idea. The waterproofing layer MUST be sloped to the drain, and that is NOT the tile. Depending on the type of drain you use, something like a clamping drain, which is probably what you have in there now, is not compatible with a surface waterproofing layer. There is definitely more than one way to produce a leak free shower, but it doesn't sound like yours got started out properly for any of them.