I am using a multisite installation (with subdirectories). I used the plugin to map domain.com and http://www.domain.com to site id 9.
This opens the myprimarydomain.com/domain site when domain.com is accessed.
All is working well except that some of my plugins are broken and css doesnt seem to work.
The moment I remove the 'primary' checkbox it works fine again.
Plugins in use: REsponsive Slider, ( I tried even meteor slides).