C# – How to stop web.config inheritance

Ok

I have a Asp .net 3.5 Website in IIS6 on Windows Server 2003 (32bit).

with a Asp.Net 1.1 WebApplication in a sub virtual directory. (this is set to use the older 1.1 .net runtime and is configured with it's own App Pool. So for all intents and purposes is completely seperate.

Except it keeps on inheriting the root website's .net 3.5 web.config.

I've tried adding

<location path="." inheritInChildApplications="false">

to the root websites web.config but it doesn't seem to work.

Strangely the error is actually

<sectionGroup name="system.web.extensions" type="System.Web.Configuration.SystemWebExtensionsSectionGroup, System.Web.Extensions, Version=3.5.0.0, Culture=neutral, PublicKeyToken=31BF3856AD364E35">

which is being reported from the .net 1.1 runtime with the website path WEBSITE/OLD_WEBAPP but it's moaning about the webSite (as in the .net 3.5 one's) web.config and how it doesn't understand the type attribute on the sectionGroup tag.

What am I doing wrong? Please tell me it's something obvious. Thanks