I've done this in the past on my hostgator account. With two subfolders, each folder assigned its own domain, Ive made multiple blogs on a shared account. However, now I have two folders both with specific domains..
lets call them folders...
/a/ and /b/
Each contains all the files needed to have a WP blog each with its own domain, however when I try to run the install in folder /b/ , I get redirected to the already installed blog in folder /a/ ... even when i goto the domain at folder /b/ , lets call it http://www.b.com , it logs me into the admin page at http://www.a.com/wp-admin