I have a web site at the root that is .net 2.0. I also have several virtual directories beneath it running .net 1 and 2.
In the web.config for the website at wwwroot I have added <location allowOverride="false" path="wwwroot"></location> and this encapsulates everything under the <configuration> node.

Now all the websites show up properly except for the root website, when I first load the page it comes up properly but when a page refresh is done I get the message below. Any ideas why this happens on a refresh?

Server Error in '/' Application.

Configuration Error
Description: An error occurred during the processing of a configuration file required to service this request. Please review the specific error details below and modify your configuration file appropriately.

Parser Error Message: Only one <configSections> element allowed per config file and if present must be the first child of the root <configuration> element.

Source Error:

Line 2: <configuration>
Line 3: <location allowOverride="false" path="wwwroot">
Line 4: <configSections>
Line 5: <sectionGroup name="system.web.extensions" type="System.Web.Configuration.SystemWebExtensionsSectionGroup, System.Web.Extensions, Version=, Culture=neutral, PublicKeyToken=31BF3856AD364E35">
Line 6: <sectionGroup name="scripting" type="System.Web.Configuration.ScriptingSectionGroup, System.Web.Extensions, Version=, Culture=neutral, PublicKeyToken=31BF3856AD364E35">

Source File: C:\Inetpub\wwwroot\web.config Line: 4

Show Additional Configuration Errors:
Unrecognized configuration section system.web.extensions. (C:\Inetpub\wwwroot\web.config line 64)

Version Information: Microsoft .NET Framework Version:2.0.50727.3082; ASP.NET Version:2.0.50727.3082