I caught my workers putting the old gross toilet ring on my new floor, ick. This is a picture of a new one. Looks suspiciously like the size might be the same.

Try sprinkling some baking soda on the floor. Let it remain there for an hour or two then vacuum it up. Hopefully, it will absorb some of the stain.

I've read about iron leaching out of marble and other natural stones but it is odd that they're all in the same area.

Have you contacted the manufacturer? They may know the culprit, or at least the best way to clean or minimize the discoloration. Good luck!

Is the tile marble? If so, the iron in marble can rust when exposed to water, can leach to the surface and cause yellowish/brownish stains. Try this link for making a poultice for removing the stain:

http://www.apartmenttherapy.com/how-to-remove-stains-from-marble-surfaces-apartment-therapy-tutorials-215702

I would make sure there is plenty of fresh air moving thru the bathroom if you use this mixture as there could possibly be some off-gassing. Good luck!

I have had this problem with marble floor surfaces and tried different poultice concoctions. The best I found was SCI. They make a rust remover version. The trick is that you have to leave it on for at least a couple of days and may need to repeat. http://shop.stonecare.com/All-Products/Cleaning---Sealing-Stone,-Tile---Grout/SCI-RPP-Stain-Remover-1-pint

I would have the plumber or another plumber reset the toilet with a new ring one more time in order to rule this out.

OK so you got a new wax ring, but was it the right size? I have seen leaks like this when the was ring was missed sized or if the flange was cracked. I agree with Norwood Architects. Because a wax ring is so cheap, I'd have it changed out and purchase it myself based on the recommendations from the toilet manufacturer. I'd also make sure that the size for the toilet and flange matched correctly.

Also cross post on Houzz Plumbing forum and see if a plumber will respond.

http://ths.gardenweb.com/forums/plumbing