Interesting, the keeping of conspec rec. is not normal in evo. sims. Especially after I looked back the dna of caterpillar, the conspec is a pretty specific check(comparing refkills with in6). Meaning with no cani-bots, there are 2 genes being unaffected.
Only reason I can find for that is the retaliation gene. Problem of that one is one mutated bot can start a chain and kill everything, like Endy said.
That random bot has a high change of being killed at once, due to the agressive retaliation gene. But if it survives long enough it can put up multiple bots "defending" against each other instead of the aggresor.
The stopping to retract, obvious comes from a broken tie moving gene, that isn't fixing or unfixing. I think that could be fixed(less affected by mutations) by having the multiple genes in a nifty formula in one gene instead of indepentant genes.
Tieing to everything, is a broken born and connect to original gene. Extra condition and it shouldn't happen. (unless the not always needed condition mutates out first)
Problem overall with hand-made bots. They didn't came out of a evolved bot, there are parts that can't handle mutations well, or in this case also an overreactive defence system that can't handle others mutating well.
Can you upload a sim-file, if you still got it? I'd like to see what happened.