Take off the toilet, take off the wax ring, and do a test fit of the toilet. Try to find out what it is rocking on, you can put ink such as from a Magic Marker on the flange (after cleaning all the wax residue off) and see if the ink gets on the underside of the toilet indicating contact there. YOu do not want any contact between the metal flange and the porcelain toilet. It is possible to make a wood or Plexiglas "ring" in the shape of the toilet footprint to be a spacer between the toilet and the floor if the flange sticks up too high.
Use shims around the base of the toilet if needed to stop the rocking. You can caulk around the base of the toilet after everything is put back in place to conceal the shims and/or spacer "ring".
A forum community dedicated to Do it yourself-ers and home improvement enthusiasts. Come join the discussion about tools, projects, builds, styles, scales, reviews, accessories, classifieds, and more! Helping You to Do It Yourself!