I have the same problem with subdirectories. My config Is:
set $sroot /usr/local/www/
location ~ \.php$ {
include /usr/local/etc/nginx/fastcgi_params;
fastcgi_index index.php;
fastcgi_param SCRIPT_FILENAME $sroot/$fastcgi_script_name ;
fastcgi_param QUERY_STRING $query_string;
fastcgi_pass 127.0.0.1:9000;
fastcgi_intercept_errors on;
break;
}

location / {
root $sroot ;
index index.php;
}

By the way I think it all happend when I've upgraded from nginx 0.9 to 1.0.11. I think that my original configs had been replaced with new ones.