Hi,
Try changing the Document root for your sub-domain to a directory that is at the same level as your primary domain. I'm not even sure they will allow you to do this. The problem is, mojoPortal can run in a root domain, root sub-domain or a virtual directory of either but it is not going to run in a virtual-directory masquerading as a sub-domain. This type of configuration is unique to GoDaddy and poses all sorts of issues with .NET applications in general, not just mojoPortal.
HTH,
Joe D.