Solved! Go to Solution.
Thanks for that information evchaps.
Issue ended up being because I missed that some of the mailboxes were hiding from the GAL, and some of the AD accounts were disabled. Disable accounts showed up as 3, and users who were hiding from the GAL but were new mailboxes were a 0. When they were hiding from the GAL they didn't show up as a new mailbox by running the enable mailboxes wizard. If only EV was smart enough to ignore the GAL, and just use LDAP, but apparently not (or I'm not smart enough).