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...
The decision doesn't have to be logical; it was unanimous.