This should be what you are looking for I have 7 sites I manage on the same server and this seems to be the fix. The problem was that I was activating the Plugin from the network admin. Follow the steps found in this link and it will work just fine. Also go the settings/reading and check Search Engine Visibility if you do not want people to be able to search for your site in search engines.
http://premium.wpmudev.org/manuals/wpmu-manual-2/activating-and-deactivating-plugins-on-a-per-site-basis/
