I think you normally don't want to produce different chromosomes/results using the same seed. That is the whole point of replicating previous runs. The same results are produced because the same "randomizer" is used.
If you want to produce a different result while using the same seed, you can choose to use some randomizer of your own. I think this might be a useful technique, say, if you want to use the same breeding process between runs, but use selection methods with different randomizer, you can implement your own randomizer in the selection methods (and you will not be using the default randomizer offered by ECJ in the selection methods).