Seems that Apple is yet to get partitioning and formatting right. One would think this used to be a DOS/Windows issue over a decade ago. Well, think again!
I partitioned and formatted my iMac HDD when Mountain Lion was released. I always like to do a clean install to make sure that there is nothing un-expected which can happen on occasion on a restore from a backup.
Everything worked fine and nothing seemed to be out of the ordinary for a while. By this time, I had filled up about 80% on the second partition with backups and downloads. Then, one day, I ran the latest update of Onyx, as I always do on any update of this wonderful free app, and to my surprise, it failed on the disk check.
The error was un-recoverable and the stock Disk Utility also had the same issue. Going through some forums, it seemed that quite a few people had encountered similar issues with no real solution listed.
I tried to re-boot the iMac in recovery mode to see if the disk could be repaired from there. Instead of booting into the recovery, as it used to, the iMac went to the internet to download something. For a moment I thought the HDD was gone as it failed to boot into the recovery. About 10 minutes later, it did go into the recovery mode and I was able to run the Disk Utility from there.
Finally, some hope…the Disk Utility corrected the partitioning issue with a message that suggested that the partition/data sizing was not done corrected and it had to resize the partition to fix the problem. So much for a tested release of an OS. I am just happy the issue was fixed and I did not have to go through a complete re-install which I had done with the Mountain Lion release.