Haven't checked for a long time, but I doubt the default settings are any good for a zerobot sim. You could try setting only morphological costs (for simplicity only number 1 in each field) in the right side of the costs dialog. Put 0 into body and DNA upkeep and have ageing turned off. Start out with 0 in costx and set a number where you want costs to start increase and decrease, depending on the level of the population. Later when you got some good replicators you can add costs to body upkeep and ageing, something like 0.00001 for instance. Let the ageing cost increase with 0.00001 every cycle. Just an example.
...and for the body upkeep cost to be any good you need to run with either autotrophs, or heterotrophs that can gain energy in some way.