When the temperature of the hard drive changes, the media expands slightly. In modern drives, the data is so densely packed that this expansion can actually become significant, and if it is not taken into account, data written when the drive is cold may not be able to be read when the drive is warm. To compensate for this, many drives now perform "Thermal Recalibration" every degree C (or so) as the drive warms up and then some longer periodic interval once the drive has reached normal operating temperature. When thermal recalibration takes place, the heads are moved and the drive may sound like you are accessing it. This is perfectly normal.
If you're attempting to access the drive when thermal recalibration occurs, you may experience a slight delay. The only time this becomes important is when you're doing real-time operations like recording / playing sound or video. Proper software buffering of the data should be able to hide this from the application, but software seldom does the proper thing on its own. Because of this, a few companies have come out with special drive models for audio/video use which employ special buffering techniques right on the drive. These drives, of course, cost significantly more than their counterparts. Some other drives offer a way to trigger thermal recalibration prematurely (thus resetting the timer), so if your real-time operation is shorter than the recalibration interval, you can use this to assure your operation goes uninterrupted. Disabling or delaying recalibration is dangerous and should be completely avoided. For more information on the thermal recalibration characteristics of a drive, contact the drive manufacturer directly.