Disk structure error reported in Onyx but not fixable via the Disk Utility in Recovery Mode

Solution 1:

I had the same issue. I was able to fix it in an interesting way.

I have been testing El Capitan on an external drive. So, I thought, why not try Disk Utility using OS 10.11.x and (after the second pass) it repaired the drive. As the Beta was on a separate disk, and the Macintosh HD was unmounted at the time, it was analyzed and repaired. Just like using a 3rd party app.

At least this was a "free" way to fix it. Saved the hassle of reformatting and restoring.

Solution 2:

Disk Utility will not fix every conceivable disk corruption issue. For that you need third-party apps. I use Diskwarrior and have also had success with Drive Genius.

However there is one way to do this without buying a disk repair utility. Back up your hard drive, partition/reformat it, reinstall the OS and restore your backup. Yeah it's more complicated and a bit of a PITA but will save you money.

Solution 3:

This was a problem for me too. I booted from an external disk (USB stick in fact), ran disk utility, then Onyx found no problems.