There is something else going on other then a flange that isn't level. Even if the flange was a 1/4" lower on one side then the other the wax seal would conform to it. Is the top of the flange below the level of the floor? If so then use two wax seals one on top of the other. Also is the flange screwed down to the floor? After you set the toilet is it sitting flat on the floor or does it rock? If the toilet rocks after being set the movement over time will destroy the seal. Concrete floors can be uneven and may require shimming the toilet after setting to prevent it from rocking.
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