Type is not declared and name is not declared errors in App_Code

Hi I have an application which I have worked on several times, but this week I've been trying to get the application to work on a new laptop and failed.
First there were was some dependency issues with some controls like the AJAX Control Toolkit and AJAX Extensions, but now that I have everything I'm still getting errors.
The errors that I'm getting are only in the App_Code classes.
For Example I have the following references in the web.config
<namespaces>
                <add namespace="System"/>
                <add namespace="System.Collections"/>
                <add namespace="System.Collections.Specialized"/>
                <add ...