You're comming from 2.3X right?
If I remember right I fixed a virus range bug in the code in 2.4 a while ago. The virus problem might be related to that.
Collision response has been quite shaky in 2.4. It's one of its problems. I don't know about the taking damage, but I routinely see bots seem to just pass through each other. Its because the collision response isn't strong comapared to their momentums. This has been fixed in the C++ version, I'm happy to say, so I don't know how much work should be spent fixing this in 2.4.
Back to the damage comment, maybe we should damage bots that collide with something too fast. That would encourage bots to watch their speed while still letting them use high speeds to escape from potentially fatal situations.
As to ties, is it tie physics that doesn't work or another aspect of ties? Ties seem to work for me better in physics than in 2.3X. Try making a bot that only reproduces once and then ties to the offspring. Drag and throw one of the bots, and you should see some rather realistic motions.