I am also experiencing this issue - and I am currently using a provisioning agent in my template (full agent installed as a last step). Like Jeff, when the template gets to the patch task it marks it a success but instantly moves on and does not actually apply any patches. I have also created a custom configuration that should pop-up a UI to see the patch task progress and it never actually happens. When I was on 9.5, the same task worked fine. Since upgrading to SP1, it no longer works.
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