Where is the toilet flange in relation to the top of the floor? Did the wax ring actually get compressed when you set the toilet? Did the toilet rock any after it was installed? It must be shimmed so it is perfectly stable, or the wax will squish in one end, and when you rock back the other way, then leave a gap...the wax doesn't rebound like a spring...once compressed, it stays that way. If the seal is good, are you sure it is not leaking between the tank and the bowl? If all else is good, then there may be a defect in the toilet, or it is damaged (cracked) and leaking there.