I've just installed your plugin on all the sites I manage. I have one that's a test site for a client and it's in a subfolder of my website. I can access the homepage, but once I click through on any of the links in the navigation, it takes me to a 404 for my website. I went through and tried to adjust the .htaccess to add in references to the subfolder, but it's still not working properly.
Is this a conflict of the plugin being installed on my site AND in the subfolder? Or is it something else I should be aware of?