Not Archiving Messages From Certain Date Range

I have a tough one, and I hope someone has a great method to get this working. I am trying to run an archive task on email that should have been archived to begin with (ran an archive task on the whole exchange server with no rules). However, when I try to search for email via the EX Search Client for a particular date range, only a small amount of email appear for a user's mailbox. When I try to run an archive task on that user's mailbox for the dates in question, it bypasses all of those email and it never gets archived. To go further, running a shortcut task (with the checkmark on for only messages previously archived) during that date range, only a handful of messages are archived. If I uncheck the only messages previously archived, all the messages gets shortcutted, but now those messages that were never archived cannot be restored.

I was reading where EX adds some tags onto the messages, and I think this is where the problem is, but I don't know how to check for these tags or how to remove them. Any and all advise will be greatly appreciated.