I had a similar situation based upon a Disk Utility report.  No matter what I did with Disk Utility, it couldn't repair the problem.  I invested in DiskWarrior 5 and used the USB to boot up my iMac.  DW fixed the problem.  I then ran DU again and it verified the problem was fixed - it didn't report a problem.  In addition, my iMac ran faster as well.