How to prevent multiple login windows?
Disable File Vault if you don't want this two step log in process. You can be sure FileVault is off by seeing the following from terminal:

Mac:~ me$ diskutil cs list
No CoreStorage logical volume groups found


Alternatively, you could disable and re-enable the File Vault encryption and watch for the prompt where it asks if the OS user should be permitted to unlock the drive with the user's password. 

If you select yes from that, the user will show up on the first login screen and both unlock the FileVault protected volume and log in with the same credentials.