New issue: Running in persistent mode and enabled encryption on the user's home directory. I also changed the auto-login script in inittab. I rebooted and was prompted with the desktop with the missing background/menu items. It seems to have auto-logged in as the user. I logged out and logged back in as the user using my own password, so far so good. I checked TTY1 and saw that the root user is logged in. Furthermore, the user is logged in on other terminals.

This isn't very secure if root auto-logs in at reboot. Kind of defeats the purpose of having a user.