Today I decided to upgrade ConfigMgr 2012 to SP1 in my lab but I ran into a problem.  My ConfigMgr server was running on Windows Server 2008 R2 Evaluation.  During the upgrade my server shutdown because it was past the expiration date.  Since I didn’t have anything of value in ConfigMgr I thought it would just be best to wipe out ConfigMgr and install it again.  I deleted my ConfigMgr VM, ConfigMgr server object in AD, and even removed the ConfigMgr instance on my SQL server.  While installing ConfigMgr I was getting an error that the dedicated instance was already being used by another ConfigMgr implementation.  No it wasn’t!  I removed the SQL instance, again, removed all of the folders in the SQL locations for it, installed a new instance(same name), and upgraded it to SP2(SQL 2008 R2).  I was still getting the same error message.  It took a while but I found a leftover registry key that was preventing me from installing ConfigMgr again even after wiping out the instance in SQL.  Maybe if I uninstalled ConfigMgr it would have worked or created a new instance named ConfigMgr2 it would have worked but oh well, I got it resolved finally.  

Below are the screenshots. 

The error was:
Configuration Manager requires a dedicated SQL Server instance to host its site database. You selected a SQL Server instance that hosts the site database for another Configuration Manager site.  Select a different SQL Server instance for this new site to use, or resolve the conflict by uninstalling the other site or moving its database to a different SQL server instance. 

The leftover registry key on the SQL server located at HKLM\Software\Microsoft\SMS

Once I deleted the SMS registry key I didn’t get that error message and I could continue working on my prerequisite failures.