Prior to mojoPortal 2.7, it was required to create the folders you wanted to use for your multi-tenant sites.
In a default configuration of IIS, a request like http://hostname/site2/ will be handled first by IIS, typically it will look for a Default.aspx file in the folder named somefolder and if it is found it will hand the request off to ASP.NET but if the folder does not exist and/or the file is not there, it will generate a 404 page not found error rather than handing the request to ASP.NET.
So if you want to have it work with urls like http://hostname/site2/ you would need to either make ASP.NET the default handler for all requests or make sure the folder exists and it contains a file named Default.aspx. The Default.aspx file can be just an empty text file, it doesn't need any code or contents in it, its only purpose is to get ASP.NET to handle the request. From there the mojoPortal code detects the folder mapped to the site and serves the correct content. Without doing one of these things, the only way ASP.NET will handle the request is if the url ends with Default.aspx or somepage.aspx where somepage.aspx is an url defined by the site.