By default, virtual directories inherit the web.config of their parent web sites. That is why "clear" is so important. There is a way to stop it though (and treat each virtual directory like a separate app): inheritInChildApplications
"Set InheritInChildApplications to false to prevent settings that are specific to a certain location (such as the root directory of a Web site) from being inherited by applications that exist in subdirectories.
The following example shows how to use this attribute in a configuration file to specify that the settings defined in the location element for the root of a Web site should not be inherited by child applications:
<location path="." inheritInChildApplications="false"> "