You have me confused as to what you have. A cultured marble shower base normally does not have a liner. Then you mention a mortar base.
If it is a tiled base with a liner, it sounds like the liner was installed without a preslope - i.e., the liner was installed flat on the floor. If that is the case, especially if the weep holes are blocked, will allow water to accumulate under the floor. If that is the case, that moisture will prevent the caulk from lasting.