Cornelius,
Overlapping extents can be a difficult problem to fix. If the extent of the problem is mild, then it may be repairable, but Disk Utility generally cannot fix overlapping extents. However, Disk Warrior can although it can take some time to repair a drive where the problem is extensive - hours to days.
It is possible to repair overlapped extents using fsck provided the problem is not too extensive. The following KB article discusses how that's done:
http://docs.info.apple.com/article.html?artnum=25770.
The following is another discussion of how to fix overlapped extents:
Manually fix Overlapped Extent Allocation Errors without Disk Warrior
Overlapped overlapped extent allocation errors can be the bane of any Mac user's existence. Often, these errors go unnoticed until the problem becomes visible: your Mac might refuse to boot, crash unexpected, or worse, critical data might disappear from the Finder. Disk Utility can detect, but not fix overlapped extent allocation errors, and certain third-party utilities, such as Alsoft Diskwarrior, can fix them, but generally without reporting the consequences.
Overlapped extent allocation error occur when the file system thinks that two files are occupying the same area on the hard disk, hence overlapping on the same "inode," which is the structure which holds the location of the data blocks the file occupies, and also file permissions and flags.
Clearing the "overlapped" or "overallocated" extent allocation essentially means that you'll have to lose some data, because the only way to remove the overlap is to delete the file that's occupying the inode. So, if you suspect, or find out, that the guilty file is a critical system file that resides in one of the hidden system directories such as /etc /var /usr/ or visible system directories such as /System or /Library, and you don't want to reinstall the whole OS (which might not fix the overlapped extent allocation anyway), it's good to have another disk available to copy the files back to your original disk if necessary: a second bootable hard drive or a firewire drive connected to your Mac when you remove the misbehaving file. Just make sure that when you copy the file back to your boot disk that the permissions are correct, so it's best to use the "ditto" command, so that all sticky bits, flags, and permissions are preserved.
In case you didn't know, you don't have to boot from an install CD in order to check for overlapped extent allocations. All you need to do is restart your Mac, while holding down command + S to boot in "single-user mode."
At the command prompt that appears, type:
$ fsck -fy
If you have an overlapped extent allocation, you'll see:
"Overlapped Extent Allocation" (File 123456d)
No matter how many times you run fsck -fy, you'll never be rid of the error.
So, simply issue the following command:
find / -inum 123456 -print
Note the "d" was dropped, or any extra letter that appears after the inode number.
The find will return a file name that matches with the inode number, and the path to that file. If you remove the file then the fsck will not return this error next time you run it.
However, before you can delete the file(s) in single-user mode, you'll need to mount the file system. Type:
$ mount -uw /
When done, issue the "sync" command, and that will flush the write cache so that all pending writes are written from memory to the disk. Also, since most OS X 10.3 Macs use the HFS+ Journaled file system, it might be a good idea to disable the journal before booting into single-user mode by typing:
$ sudo diskutil disableJournal /
then re-enable it when done fixing the overlapped extents and rebooting normally:
$ sudo diskutil enableJournal /
Chris Anderson is a long-time Linux propellerhead who just got his first Mac, an ibook G4, and can't keep his hands off of it. He currently works as a "The Architect" and general visionary for a maker of world-class collectibles.
If the problem is not fixable then reformatting the hard drive is the only other way to repair the drive.