Mac OS X: Disk Utility incorrectly reports disk errors on startup volume (disk)
Start up from your Mac OS X install CD or DVD to use Disk Utility when you need to verify or repair the Mac OS X startup volume.
Disk Utility, Mac OS X 10.0, Mac OS X 10.1, Mac OS X 10.2, Mac OS X 10.3, Mac OS X 10.4, Mac OS X 10.5
Otherwise, Disk Utility may report errors on the Mac OS X startup disk, but not find errors on the same disk when started up from a Mac OS X disc.
Start up your computer from the Mac OS X CD when you need to use Disk Utility to verify the Mac OS X startup disk. (This is the most common use of Disk Utility.)
If the computer is started up from the Mac OS X hard disk (or disk partition) and Disk Utility finds errors on it, there is not necessarily anything wrong. Only when started up from the CD should Disk Utility reports of errors on the Mac OS X hard disk (or disk partition) be considered accurate.
Mac OS X 10.4.2 and earlier do not allow you to verify or repair the startup disk with Disk Utility. With Mac OS X 10.4.3 or later, you can verify your startup disk using Disk Utility. To repair the startup disk in any version of Mac OS X, start up from your Mac OS X Install DVD or CD.
For more information on using Disk Utility and fsck for file system maintenance in Mac OS X, please see this article.