There is an option to avoid this if you are using the RB3011 for routing.
You can setup queue to let the CPU limit the amount of packets that can pass through at a certain time.
add max-limit=90M name=Limit_Gigabit_to_Fast packet-mark=Gigabit_to_Fast parent=global
/interface list member
add interface=ether2 list=FastEthernets
/ip firewall mangle
add action=mark-packet chain=postrouting new-packet-mark=Gigabit_to_Fast out-interface-list=FastEthernets