You don't mention the url structure for the support app. If its really a separate IIS site with a separate host name like support.yourdomain.com, there should be no conflict. If its not really a separate site but a virtual directory beneath the mojosite then the web.config for mojoportal since it is in the root interferes with the web.config settings for the child app. There are ways around it using a <location> element in Web.config to wrap some of the mojoportal settings and limit their scope. If you do some googling about the location element you will find solutions for similar problems as this can be an issue anytime you have one .NET app in the root of a site and another in a virtual directory beneath it.
Hope it helps,