I had exactly the same problem.
Ask for a “jumbo” wax ring at the
plumbing supply store. It is thicker and has 50% more wax
to compensate for the added
thickness of the tile.
Also, as a sideline, make sure the
metal flange ring that holds the
bolts that secure the toliet bowl
are tight. I had to reset the
ring with concrete anchors to the
foundation because the orignal was
only put in place with 1″ nails.