Microsoft SQL Server 2008 R2 Best Practice Analyzer fails with “Engine - Login does not exist or is not a member of the System Administrator role”

If the Windows account you are using for SQL BPA to connect and analyze an instance of SQL Server Database Engine doesn’t have an individual login created in the instance and that login is a member of the System Administrator server role, you will get that error, even if the login has been made a member of sysadmin via its membership to a Windows Group login which is member of sysadmin.

This is a flaw in the UA tool and there’s no current fix for it, neither plans to get it solved in the near future. So, proceed with the workaround which consist of creating a login for the account, and making it a member of sysadmin server role.