After some research we found that all users that were missing weren't SIP enabled or didn't have any telephone number assigned within Active Directory.
So I decided to play around with the ABS Configuration Tool to see if we can fix the issue.
The first thing that i noticed was the "Is this Attribute Required?" tick-box.
I wasn't able to find anything that explained how this was working as there are multiple "AD Attribute Name" with this tick-box enabled.
After some playing I "think" I figured out they acted like an "OR" statement, so as long as a user account, contact object or group has one of the values "required" Lync would reference them in the address book update.
The following TechNet article on Administering the Address Book Service has a nice description of what can be referenced in the address book.
The ABS Configuration tool can be found in the Lync 2013 Resource Kit Tools, the Lync Server 2013 Resource Kit Tools Documentation has all the details on the tools, there is a word file in the download but there are things wrong that you notice off the bat, the image from the ABS Configuration tool is actually from the Lync Stress tester.
