I have installed a new site with SQL database(R2 SP1). I have NOT selected the public templates option. Browsing the site gives an error stating only core files has been installed. This is expected behaviour. But when I have copied some templates folder to the deployment root from another site installed, problem i am facing is there are 2 "start" appearing under the "Root" tree. Actually as I guess, since I installed a new SQL database, It should be empty if I have unselected public templates option right?
You are correct, if you install a new database and don't install the public templates you should get an empty site (just the root and a wastebasket).
Could it be that when you copied your templates you copied your connectionStrings.config as well? Because it seems like your site is using a database where the default content has been installed twice.
Either that or you selected to install content twice from the page /ui/admin/setup.aspx.
Per GunsarfsEPiServer CMS development team