If disk Utility can't do it just boot in single user mode and use the fsck command. Quicker than booting from your install disk. Dunno why Apple wants to tell you you shouldn't or you don't have to. Ignore them.
It's not a bad idea to occasionally verify the HD, using disk utility on the installation disc. Don't use the disk utility on the HD - it can't verify itself! 🙂
'Fraid it can't! That's exactly why OP was warned to run Disc Utility from the Install Disc!🙂
See also what Apple say:-
"Try Disk Utility
Start from your Mac OS X Install disc: Insert the installation disc, then restart the computer while holding the C key.
When your computer finishes starting up from the disc, choose Disk Utility from the Installer menu. (In Mac OS X 10.4 or later, you must select your language first.)
Important: Do not click Continue in the first screen of the Installer. If you do, you must restart from the disc again to access Disk Utility.
Click the First Aid tab.
Click the disclosure triangle to the left of the hard drive icon to display the names of your hard disk volumes and partitions.
Select your Mac OS X volume.
Click Repair. Disk Utility checks and repairs the disk. Tip: Always start up your computer from an Install or Restore disc when using Disk Utility to verify or repair your startup volume. Otherwise, you might see some disk error messages."