I ended up following the instructions to completely remove BlackBerry Professional Software from the server, including the REGEDIT parts, rebooted the server, then reinstalled from scratch. It now works perfectly. Thank you everyone for the assistance.
Sorry to hear you had to build the server from scratch. The problem you were having is that the database had more users, while the BlackBerry Manager wasn't displaying the correct number of users. In the future, if you face this issue again, run the following on the command prompt (in the following order):
1- osql -E 2- use besmgmt (or whatever is the name of your configuration database) 3- go 4- select mailboxsmtpaddr from userconfig 5- go
This will list the email addresses of all users added to your server. Once you are able to identify the user who you don't want on your server, run the following on the command prompt (again in the same order):
1- osql -E 2- Use besmgmt 3- go 4- Delete from UserConfig where mailboxsmtpaddr ='firstname.lastname@example.org' 5- go
This will remove the unintended account from your BES/BPS database.