Does my MU install need to be on root for plugin to work?

Server: Bluehost (shared)
IP: Dedicated
WordPress install: Multisite, but not on the root directory
Plugin: Installed correctly (according to instructions)

My site works great, except for when I try to map a domain to it. Instead of directing the domain to, the site I want, it directs it to the site on the root directory (which by the way is not WP).

Does my install need to be on the root in order for domain mapping to work?

MU Site: