[U2Lynne]

Here are a couple of articles/documents to explain encryption:

Encrypting Bittorrent to take out traffic shapers
BitTorrent protocol encryption

However, notice this part under the second link:

Many ISPs are now using more sophisticated measures (such as Deep packet inspection) to detect BitTorrent traffic. This means that even encrypted BitTorrent traffic is now throttled. However, for those using primitive methods to identify and throttle BitTorrent, the current solution remains extremely effective.

So, you may want to make sure you are always downloading the latest versions of your clients to stay ahead of these "more sophisticated measures." (Although, if it's just the university, they may not always be keeping up-to-date on this throttling.)