It actually makes sense for the bots to duplicate important genes(yes, they do). Normally they form a Highly Mutated and Largely Unmutated combo. The largly unmutated gene will be later in the genome, while the earlier one is freer to diversify. Mainly it stems from the linear nature of dna processing, not a problem IMO as evolution works about the same.
Have some results from my oddball alzheimers/replicators. The first things they discovered were to use setaim at birth, and to randomly zero memory locations. The setaim evolution makes sense because it allows the bots to not be blocked from reproducing by their own parent once they have been born. The random zero'er managed to unfix itself, allowing it and it's decendents freedom of motion again. Interesting to note that although alzheimers' randomizing effects created the mutations, the mutations actually minimized the effect of alzheimers.
I still haven't seen a good old .repro command pop-up. Holding out hope though.