Actually your Session["SuperUser"] is null and you are checking Session["SuperUser"].ToString()
which is not converting the null value to ToString()
you have to manage like this:
if(Session["SuperUser"]!=null)
{
if (Session["SuperUser"].ToString() != "true")
{
MasterPageFile = "~/Site1.Master";
}
else
{
MasterPageFile = "~/Site2.Master";
}
}
else
{
}