Hi frist44,
From your description, I understand that you have deployed the web application to the virtual directory in the WSS 3.0 website. After inputting the login information and click button to login, the page redirects to the WSS site. If there has been any misunderstanding, please let me know.
In general, WSS site has its own web.config file which inherits and overwrites some settings of the machine level web.config. The virtual directory in this website inherits these settings, so that we encounter this issue if we don’t overwrite them explicitly.
For example, please check the following sections of web.config in the WSS website:
<httpHandlers>
<remove verb="GET,HEAD,POST" path="*" />
<add verb="GET,HEAD,POST" path="*" type="Microsoft.SharePoint.ApplicationRuntime.SPHttpHandler, Microsoft.SharePoint, Version=12.0.0.0, Culture=neutral, PublicKeyToken=71e9bce111e9429c" />
<add verb="OPTIONS,PROPFIND,PUT,LOCK,UNLOCK,MOVE,COPY,GETLIB,PROPPATCH,MKCOL,DELETE,(GETSOURCE),(HEADSOURCE),(POSTSOURCE)" path="*" type="Microsoft.SharePoint.ApplicationRuntime.SPHttpHandler, Microsoft.SharePoint, Version=12.0.0.0, Culture=neutral, PublicKeyToken=71e9bce111e9429c" />
<add verb="*" path="Reserved.ReportViewerWebControl.axd" type="Microsoft.Reporting.WebForms.HttpHandler, Microsoft.ReportViewer.WebForms, Version=8.0.0.0, Culture=neutral, PublicKeyToken=b03f5f7f11d50a3a" />
</httpHandlers>
<httpModules>
<clear />
<add name="SPRequest" type="Microsoft.SharePoint.ApplicationRuntime.SPRequestModule, Microsoft.SharePoint, Version=12.0.0.0, Culture=neutral, PublicKeyToken=71e9bce111e9429c" />
<add name="OutputCache" type="System.Web.Caching.OutputCacheModule" />
<add name="FormsAuthentication" type="System.Web.Security.FormsAuthenticationModule" />
<add name="UrlAuthorization" type="System.Web.Security.UrlAuthorizationModule" />
<add name="WindowsAuthentication" type="System.Web.Security.WindowsAuthenticationModule" />
<add name="RoleManager" type="System.Web.Security.RoleManagerModule" />
<!-- <add name="Session" type="System.Web.SessionState.SessionStateModule"/> -->
<add name="PwaAuthentication" type="Microsoft.Office.Project.PWA.PwaAuthenticationModule, Microsoft.Office.Project.Server.PWA, Version=12.0.0.0, Culture=neutral, PublicKeyToken=71e9bce111e9429c" />
<add name="PublishingHttpModule" type="Microsoft.SharePoint.Publishing.PublishingHttpModule, Microsoft.SharePoint.Publishing, Version=12.0.0.0, Culture=neutral, PublicKeyToken=71e9bce111e9429c" />
<add name="Session" type="System.Web.SessionState.SessionStateModule" />
</httpModules>
We should clear the settings defined in web.config for the WSS site, and readd them with the default providers. We can compare them with the machine level config file which is: "C:\WINDOWS\Microsoft.NET\Framework\v2.0.50727\CONFIG\web.config". For more information about this issue, please refer to the following link:
How to: Modify Configuration Settings for an Application to Coexist with Windows SharePoint Services
http://msdn2.microsoft.com/en-us/library/ms433526.aspx