Today I’m upgrading the rest of my System Center products in my lab to SP1.  I have some VMs that were RTM and some that are Beta SP1.  When upgrading Orchestrator I received an error message saying “Setup detected that all Orchestrator features are already installed on this computer”
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The reason why I got that error was because Beta SP1 was installed.  There is no upgrade paths from Beta SP1 to SP1 so you have to uninstall Beta SP1 and install SP1.
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I had to uninstall the Orchestrator Runbook Designer Beta SP1 and Orchestrator Management Server Beta SP1.  Just to make sure anything Beta SP1 was not on my SCORCH box I also uninstalled the Orchestrator Runbook Server Beta SP1 and Orchestrator Web Features Beta SP1.  After all of that I was able to install System Center 2012 Orchestrator SP1 and all of my runbooks and settings were still there!