I've been paying attention to my CPU usage and at present (middle of the day, almost nothing going on) it's very high (like 80%). If you look at the running applications, there is nothing to indicate what this usage is coming from. If I had to guess, I'd say Windows is probably doing something with file replication or indexing or something, but there is no indication that this is going on. Is this the case, and if so, is there a way that the application or thread could be shown to the users? Could there be a status display just saying if the server was doing something or something? Right now the activity is almost indistinguishable from a virus or something.
During this time, if you open Task Manager, and click View -> Select Columns... In this window, check "I/O Write Bytes," and "I/O Read Bytes", see if you notice any particular thread doing a great deal of disc access. Please let us know what evidence Task Manager provides.