Unfortunately the location directive only works in server context, so fastcgi_param SCRIPT_FILENAME is always going to loose
any http context defined vars for executing php and perl scripts, basically where they are needed.

Would be nice to be able to set location in http context for those perl and php scripts as I have them, making them server wide for vhosts.

I'll take your other suggestion for now and just use another include file so I stop having this issue with freebsd overwriting that file.

Thank-you.