I built a command block circuit (please look at screenshots), which should give you an egg and take a rotten flesh (for an adventure map). Circuit 1 works as expected (gives you an egg for a rotten flesh), but Circuit 2 gives you two eggs while you still give one egg. Also, the whole thing doesn't work when there's an repeater behind the comparator.
Note: In the screenshots there is Facing: east (Towards positive X)