We have experienced leaks around the base of our bathroom commode since we moved into our house about 10 years ago and have replaced the wax seal several times. The floor is now wet and spongy in that area and the tile has begun coming up to reveal another tile floor underneath (My guess is that this is a problem that antedated our move and it was tiled over to conceal it). We are now replacing the commode with a new one and replacing the wax seal once again, as my husband says we cannot do anything about the floor until it dries. Should we wait till it dries? Then what?
If the floor is spongy as you indicated, then I'd suggest replacing the plywood subfloor around the toilet. It sound like the plywood has become saturated from all of the leaks and has rotted. You'll just need to cut out the area which has rotted and lay down new plywood, this will provide a steady floor so the new toilet will not rock and damage the wax ring causing another leak. It's not a very tough job, and could be easily done on a Saturday or Sunday. Good Luck!