New flooring raises the floor level by 1/4 to 3/4 inch. The toilet flange stays where it was -- now it is below the finished floor instead of flush with it. The toilet base sits on the higher floor but the bolts anchor to the lower flange. Result: the toilet rocks, the wax ring cannot seal properly, and you get leaks or sewer gas. This is one of the most common issues after a bathroom floor renovation. The fix is a flange extender to raise the flange to match the new floor height, plus new shims and a fresh wax ring.