I am a newbie in this but... I have a lot of trouble like you have... I found (I don't know if I am correct or not) that if you try to use a PHP script made for PHP_MOD using FastCGI, it will not recognize the script... because a lot of variables in the .php are set for an specified PHP MOD (for example, in roundcube you will find in a .htaccess the block IfModule mod_php5...
Maybe you can add a handler in a .htaccess of your program, forcing the PHP mod that you want to always run "AddHandler whatever .php"
I hope this help you
edit: it looks like you have a permission problem, so... the application can't read the .htaccess (which has his own directives) and cgi can't process it, so it is offered you to download as a not recognized file.