It sounds like one of the patches you are installing is not having its reboot supressed. You could try and do a "shutdown /a" as post command but it's unlikely to work as the job doesn't sound like it is completing at all.
You're best off trying to track down which patch by looking on the target that is prompting and checking the running processes. Hopefully you will be able to see the patch running. I'd suggest you try that patch on its own and if you get reproducible results then raise it with support.