Had that same problem in my old place. Wondered why the toilet rocked after changing the toilet. A few years later I remodeled that bathroom, and installed laminate flooring over the entire floor. Small bathroom, maybe 4' x 5'. Had to get longer flange bolts, but his time it gave the toilet a flat surface o rest on. Problem solved LOL, after a few years and a remodel. I would suggest either shimming it or looking for a toilet that has a taller base flange, enough to accommodate the height of you drain flange. Plumbing sucks, toilets suck even more!