Domains do not point to folders, they point to ip addresses.
mojoPortal can run just fine as a root IIS web site or in a sub folder virtual directory in IIS, what it cannot do is run in a sub folder and pretend it is a root site like some hosts (GoDaddy) does with domain forwarding or domain masking
This is what you site appears to be installed like. When I view the source of the page I see the csshandler url is:
'/isitjust/csshandler.ashx?...
which means your site is not really running in a root level IIS web site, it is not duplicating the domain name it is using the folder that it is running in as part of the url which is only natural.
There is no way it will work correctly in that kind of configuration.