Again, it's Muller's Ratchet, and it's not a problem with the simulation per se, it's a problem with real life (which DB is a subset of (or tries to be anyway)). You can decrease the effects of Muller's Ratchet by lowering the mutation rates, but you'll never be able to totally eliminate it (at least I don't think, I won't pretend to be an expert in this area, I only had basic college bio and what I've researched myself, so there are quite a few holes.).
In real life, the population size for asexual organisms on the planet is simply so large that Muller's ratchet isn't strong enough to eliminate life. Also, the muation rate is apparently low enough as well.
Once you introduce sexual reproduction, Muller's Ratchet is defanged, so to speak, which seems to me to be the real reason macro-organisms go to all the trouble to do it in the first place. There simply aren't enough whooping-cough monkies in the world to compensate for Muller's Ratchet through asexual reproduction.