Autologon is set for provisioning, and then turned off. This is commong in RIS based and VM based provisioning situations. It is only needed to kick off some actions after the OS is laid down to install necessary applications which will then run as services. BBSA does not need autologon to run jobs.
How about during patches? We're seeing odd things during our patch runs that may indicate the server is waiting for a reboot, however, the jobs just keep running, regardless of the fact that the patches are actually installed.
Your problem isn't autologin - your problem is that when you join your domain a login banner is set and that is preventing autologin from running.
have you tried running the domain join in the 'post-install' tab of the system package (not a post-install batch job but in the free text area in the system pakcage)? this should put the domain join in the runonce that runs after the auto-login has occured.
how are you running your patch application? did tony give you the pajwrapper script yet? that should take care of the patching issue.