Recently built myself a new server for my home lab and decided to build out a new domain. During the setup process of CM12 SP1 (on Win 2012 with SQL 2012 SP1 CU2), the guest VM hung midway through setup and was completely unresponsive. So I reset the VM and ran the CM12 SP1 setup again – it only allowed the site to be uninstalled, which I did. However after immediately trying to install CM12 again, I received error “Another copy of Configuration Manager Setup is already running”.
Just restart the server after the uninstall of the site.