This happens on some of my Ubuntu servers but not all. I just did a fresh install of Ubuntu server 12.04 and when began to install updates, my 600kb/sec download speed is suddenly cut to 3kb/sec after several seconds.
This happens irregardless of whether I use a bandwidth-limiting client like wondershaper.
I believe that this is an Ubuntu problem, as none of my other servers are experiencing this, including servers running other distros.
Any help is greatly appreciated!