lorax - 4:02 pm on Dec 4, 2012 (gmt 0)

And you're sure the physical files are in a completely separate directory? I ask only because it's acting like htaccess for one is affecting the other. And if you did create two separte installs then there should be no changes to the wp-config.php files other than is necessary for a single install to work (eg - no MultiSite)