The "problem" you are noticing is that most software is not programmed to take advantage of multiple execution cores.
The problem in a nutshell is that writing parallel execution routines in software is not trivial.
What you point out is exactly the problem that many have been "freaking out" about for a while. That multi-core is all fine and dandy for workloads that can leverage parallelism. But for a lot of applications this is very difficult to accomplish.
In the case of this "computer" at this university, it's likely a number crunching "computer" or supercomputer. Very likely to be just a gang of machines networked together to process ridiculously parallel problems.
Not something you'll ever boot Vista on and expect to run Half Life any faster on...