The 'reset password' utility has changed over the years, here are my stock instructions for it on 10.9…
Backup before you begin just in case.
Boot holding cmd+R. Recovery mode should startup (assuming you have a recovery partition).
Select Terminal from the Utilities menu.
Enter the word…
resetpassword
… & hit return.
The GUI app will open, select the main boot HD.
Select your user account in the popup menu.
Then click the Reset button at the bottom right. It will "Reset Home Folder Permissions & ACL's"
Repeat for the other users.
Quit ResetPassword from the menu, then quit Terminal & reboot
That will change the permissions inside your user(s) home folders. These are not normally changed by Disk Utilities repair permissions because packages don't usually install into home folders. I'd be a little more worried if this didn't work for you since it probably just applies a few rules to set the permissions (it's not using the receipts database).
I'd also try a safe boot to see if it will repair in that mode.
Safe mode https://support.apple.com/kb/HT1455 (certain things won't work in safe mode, it is normal, the OS will disable 3rd party & non-essential system extensions).
Then reboot & try again (to see if safe mode cleared caches that effect repair permissions).
I have a feeling safe mode won't make any difference 😟
Sorry this is weird. Leave the issue open & ask again in a week or so (to make it float to the top) someone must have seen this before.