CGI includes not working after migration to new server. - nginx

I have a couple applications (PDG Stores) running on a Plesk server running Apache both of them use a CGI include to run a php script that builds their menus. Upon moving to a new server Plesk12 Odin + Nginx + Apache none of these includes work any longer.
Not sure where to start here, is it Nginx, Apache? or SeLinux?
there are no errors in any logs at all, includes fail silently.
the Apache include module is enabled
Not sure how to troubleshoot for Nginx or SeLinux
Has anyone else had this issue?

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