This could be done many many many ways. They could be doing packet inspection, they could be whitelisting certain servers, they could be blacklisting certain protocols, etc.
pfsense is a cool router distro based on BSD that offers some interesting traffic shaping features. I don't think they're that sophisticated, but I also don't know for sure how they are implemented, so maybe they're epic afterall.
If you wanna get around it, I suggest you rent a cheap VPS somewhere, like here, and then proxy torrent traffic through it. If you use something like a socks proxy (
ssh -D [port number] [username]@[ip of your vps]) then they're gonna have a fairly impossible time legitimately identifying what that traffic is by anything beyond quantity of traffic. If they still throttle that, then I'd probably suggest you go get a job in their IT department ;P