Disk Utility in Recovery HD does not see same problems as Normal Mode

Question

[Please note my computer specs are below]
I recently upgraded to Yosemite and installed Avid Media Composer 8.2. Right after the installed the software I ran Disk Utility's Verify Disk and received the following messages after 60 seconds or so:
Incorrect number of file hard links
Volume bitmap needs minor repair for orphaned blocks
Invalid volume free block count
The volume Macintosh HD was found corrupt and needs to be repaired.
Error: This disk needs to be repaired using the Recovery HD. Restart your computer, holding down the Command key and the R key until you see the Apple logo. When the OS X Utilities window appears, choose Disk Utility.
I restarted using Recovery HD and ran Verify Disk again. It finished scanning in about one second and said everything was okay.
After restarting I ran Disk Utility a third time and received the same error messages as above.
I've just finished calling Apple support and they couldn't help me. The gentleman said it must be an anomaly because I'm using a flash disk. After several minutes it was clear he wasn't going to help me - so here I am. Computer specs below.
MacBook Pro (Retina, 13-inch, Late 2013)
2.8 GHz Intel Core i7
Intel Iris 1536 MB

Answer 1

Do this:
1. a. Resetting your Mac's PRAM and NVRAM
    b. Intel-based Macs: Resetting the System Management Controller (SMC)
2. Restart the computer in Safe Mode, then restart again, normally.
3. Reinstall Yosemite without erasing the drive:
Boot to the Recovery HD: Restart the computer and after the chime press and hold down the COMMAND and R keys until the menu screen appears. Alternatively, restart the computer and after the chime press and hold down the OPTION key until the boot manager screen appears. Select the Recovery HD and click on the downward pointing arrow button.
Repair the Hard Drive and Permissions: Upon startup select Disk Utility from the main menu. Repair the Hard Drive and Permissions as follows.
When the recovery menu appears select Disk Utility. After DU loads select your hard drive entry (mfgr.'s ID and drive size) from the the left side list.  In the DU status area you will see an entry for the S.M.A.R.T. status of the hard drive.  If it does not say "Verified" then the hard drive is failing or failed. (SMART status is not reported on external Firewire or USB drives.) If the drive is "Verified" then select your OS X volume from the list on the left (sub-entry below the drive entry,) click on the First Aid tab, then click on the Repair Disk button. If DU reports any errors that have been fixed, then re-run Repair Disk until no errors are reported. If no errors are reported click on the Repair Permissions button. Wait until the operation completes, then quit DU and return to the main menu.
Reinstall OS X: Select Reinstall OS X and click on the Continue button.
Download and install the 10.10.1 update    
Note: You will need an active Internet connection. I suggest using Ethernet if possible because it is three times faster than wireless.
Also see:
Reinstall OS X Without Erasing the Drive
OS X Yosemite- Reinstall OS X
     Note: You will need an active Internet connection. I suggest using Ethernet
                 if possible because it isthree times faster than wireless.