Under an App in IIS 6.0 or newer version, if you add a virtual directory, it uses the web.config file of the parent, thie may cause problems in some cases. You can add app under a web site in 7.0 but in 6.0 it is not possible.
To prevent child app inheriting parent web.config, put your config notes within “location” tag. See below:
<location path=”.” inheritInChildApplications=”false”> your-settings </location>
<location path=”.” inheritInChildApplications=”false”>