FUD indeed passes malware scans but FUDs change all the time, so its impossible for 1 virus to stay in your system for longer time.
as soon as file gets 2-03 tiems to virustotal the FUD is crushed.
so this is not as simple to spread as people think but of course loads of machines are infected.
That's why the RAT client has the option "update server". If you recrypt every two days or so, and with 3 mouseclicks update all your bots, no need to worry about it...