ASPRunner.Net Build overwritting web.config

I have noticed when building my ASPRunner.Net project (latest build 22849) that it adds a line in the web.config
<authentication mode="None" />
This is unfortunate as it overwrite any changes that i have done in IIS (to enable Windows Authentication)
I have enabled the 'hardcoded' login to get a login.asp page to be able to add the following code for "single-sign on"
if (MVCFunctions.GetRemoteUser())

{

XSession.Session["UserID"] = MVCFunctions.GetRemoteUser();

XSession.Session["AccessLevel"] = Constants.ACCESS_LEVEL_USER;

MVCFunctions.HeaderRedirect("menu");

}
All works fine, until the next 'build'...