Installing tile over vinyl is most often a mistake resulting in exactly what you have found. Under the vinyl may be a thin layer of plywood that was installed when the vinyl was installed and must also be removed. In fact THAT plywood if it is there is one of the biggest culprits next to deflection.
The next issue is movement of the structure (deflection). It sounds as if this has been your problem if the installation has cracked along the tile-backer seams.
Before a new installation is made the structure should be appraised for its suitability of a tile installation.
What is the size of the floor joists?
What is the spacing of the floor joists?
What is the unsupported span of the floor joists?
What is the species of the floor joists?
What is the subfloor covering the joists made of?
Whith this information a determination can be made.
