I found it, and it most certainly is a bug!
My migration process consists of many mail forwards (I'll have to write about that at some point, as it makes for a flawless migrataion).
For all of the accounts in zimbra, i have a foward that points back to my old mail server. For this account I made a typo in my alias. I would normally type in the username, and choose my subdomain in the dropdown box.
ie:
user@domain.com, would alias to
user@zimbra.domain.com.
I accidentally created an alias of
zimbra.domain.com@domain.com.
While this is a typo, it is also a bug, as the above address is valid. The second I fixed this alias I was able to log in.
Problem A: A bad alias prevents users from logging in.
Problem B: The zimbra admin interface allowed me to put in a "bad" alias
Problem C: The "bad" alias wasn't technically bad. Perhaps it is too long for zimbra, or zimbra doesn't handle more then one "." in the user portion of an email address?
None the less I'm happy I got it working now.