Are you sure it's the floppy drive you hear and not the hard drive?
Is the floppy drive light flashing when you hear the noise?
Have you cleared the recent documents list from start menu? One of your applications could be looking for a file on a floppy that is no longer present.
We have a desktop with a floppy disk drive that keeps making noises constantly when we are using the desktop. It makes noise even when we are not accessing the floppy disk drive. What could have happened?