I just had this problem again upgrading to the latest build. I tried your suggestion of deleting the old site and application pool and re-adding according to the linked article.
I also verified the correct permissions for the `MRS` folder (I had to add full access for "NETWORK SERVICE").
Unfortunately, after all that, I still got the same "403.1" error. After I went in and enable script permissions, then I got a `403.14 - The Web server is configured to not list the contents of this directory` error. Then I went and added `Default.aspx` to the default documents (it only had `Default.asp`) and then I got the following Smartmail Oops error...
System.NullReferenceException: Object reference not set to an instance of an object.
at SMWeb.Login.Page_Load(Object sender, EventArgs e)
at System.Web.UI.Control.OnLoad(EventArgs e)
at SMWeb.HelperClasses.CustomPage.OnLoad(EventArgs e)
at System.Web.UI.Page.ProcessRequestMain(Boolean includeStagesBeforeAsyncPoint, Boolean includeStagesAfterAsyncPoint)
Then I tried deleting the application pool and site again and doing a re-install so the SmarterMail installer could re-add the site, but back to the same `403.1` error.
So then I went back and enabled the script permissions as I described in this thread above and then the site started working. :/
Any suggestions for what to look for or how to cure this issue once and for all so that my server does not go down every time I do a Smartermail upgrade?