Though I haven't used it, I believe that ntop is a passive observer, and only collects information as it passes by on its own. NMap, however, will actively go out and do queries to find the information, and process how the computer's reply. Because of that, NMap is more reliable. If I'm wrong, NMap is still generally more reliable, because its been tested out the wazoo.

Ntop is based off of libcap...are you running both, and if so, from where in relation to each other?

Most universities, BTW, strictly forbid running any sort of server behind the fire wall, including file sharing programs that run only on the school's server, and furthermore specifically rule out the illegal sharing of movies, music, and games. It is rarely enforced, but it such a big deal these days that a large college or university simply can't afford to not forbid it.