Okay, I think I figured it out, I see in LastLoginTimes.xml file, the people that aren't working, are all lowercase, however the new user I added, is in proper case, example TestUser1@domain.com
I think an older version of SmarterMail originally wrote to the LastLoginTimes.xml file as all lowercase when it should of been written matching the case. So the UI reads the info in that file to display when they last logged in, and it isn't seeing the user due to case sensitivity.
Solutions? I could try and find all users with any uppercase letters and edit the file manually, or is this something SmarterTools wants to fix any time soon?
I have not edited my LastLoginTimes.xml file to make sure this can be replicated. I may do this during off peak times though, and will post my findings.