My university's physics department did the same thing with SETI@home. The SETI@home guys were smart enough to make their program run as a screen-saver that displayed Fourier Transforms so people thought it made the lab look more sciency and left it on.
Another important note is that SETI@home actually did stop running when you were using the PC. If you left Task Manager up, you could see the difference on the CPU usage graph.
