Base URL Issues

I have set up my Entity Reference View Widget according to the specifications. Everything works as expected up until the point when I click the buttons "Add Item" or "Add Items and Close Window."

The site was set up at www.example.com/site. I have made the necessary adjustments to my htaccess and settings.php files to reflect the fact that the site is installed in a subdirectory. Now this is going to sound strange but, when I click "Add Item" it essentially pushes the content from www.example.com to the "Selected Items" list. The content is from entirely different site on the same server, and in no way linked to my new Drupal site. I have never encountered anything like this before with another Drupal module. When I ultimately save the node, nothing shows up in the Entity Reference field.

When I created a subdomain for the directory, the module worked perfectly. Any ideas what could be causing this?