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Note from the moderator (me): It would be easier to address your issues if you created two separate threads in the future. For now I'll leave it be.
1) Auto-remediate only creates the job(s). When setting up the job before hand, you can check the box for Execute-now, and the patch deploy job(s) will kick off once it is created.
2) I suspect you have a permissions issue. Either you're not mapping to the Local Administrator, or there could be a security policy restricting the right to reboot. This thread has some good info on how reboots occur on Windows machines: http://communities.bmc.com/communities/message/133696
I'm not sure how but the 'Execute Now' checkbox had become unselected. That was the problem with the jobs not running. I ran into this same issue with the patch jobs I created for both W2K3 and W2K8 so I'm not sure what I could have done to cause it. They both worked as I had intended initially.
Is there a log file where I could check to make sure its mapping to Administrator? A job with the same settings will successfully reboot a W2K3 server but not W2K8. Both the domain and local policies should be fairly vanilla so if something in W2K8 is preventing a reboot I would think it would be a common issue.
You can determine what account the agent is mapping to by running the agentinfo command from the NSH prompt.