permalink problem on nginx

I read Codex > Nginx and succeeded to have network install (subdirectory).

But I have two problems with permalink settings ( https://example.com/wp-admin/options-permalink.php ).

First, I see a slug /blog before input area.
Second, there is a slug /index.php/ in the input area.

Please see screenshot.

I can’t get rid of either of them.
(/blog is uneditable, and /index.php/ appears every time even I submit without /index.php/…:( )

I have these problems only at the main (blog id = 1) site.

Please if you know how to fix it, please let me know.

Here is my nginx config files.

nginx.conf:

user              nginx;
worker_processes  2;
error_log  /var/log/nginx/error.log;
pid        /var/run/nginx.pid;

events {
    worker_connections  1024;
}

http {
	include	/etc/nginx/mime.types;
	default_type 	application/octet-stream;
	access_log	/var/log/nginx/access.log;
	sendfile        on;
	#tcp_nopush     on;
	keepalive_timeout  3;
	#tcp_nodelay	on;
	gzip  on;
	#client_max_body_size 13m;
	index      index.php index.html index.htm;
	log_not_found off;

#	Upstream to abstract backend connection(s) for PHP.
#	upstream php {
#		server unix:/tmp/php-fpm.sock;
#		server 127.0.0.1:9000;
#	}

	include		sites-enabled/*;

	server {
	listen       80;
	server_name  example.com;
	root /var/www/vhosts/example.com;

	if ($http_host != "example.com") {
		rewrite ^ https://example.com$request_uri permanent;
	}

	include global/restrictions.conf;
	include global/wordpress-ms-subdir.conf;
	access_log /var/log/nginx/colog.jp.access.log;

	}# end server{}

}# end http {}

global/wordpress-ms-subdir.conf:

# This order might seem weird - this is attempted to match last if rules below fail.
# https://wiki.nginx.org/HttpCoreModule
location / {
	try_files $uri $uri/ /index.php?$args;
}

# https://j.mp/ni5J6W
##necessary if using a multi-site plugin
server_name_in_redirect off;
##necessary if running Nginx behind a reverse-proxy
#port_in_redirect off;

# Add trailing slash to */wp-admin requests.
rewrite /wp-admin$ $scheme://$host$uri/ permanent;

# Directives to send expires headers and turn off 404 error logging.
location ~ .*\.(txt|xml|html?|jpe?g|JPE?G|gif|GIF|png|PNG|swf|SWF|wmv|WMV|flv|FLV|css|CSS|js|JS|inc|ico|gz) {
	expires 24h;
	log_not_found off;
	break;
}

# Pass uploaded files to wp-includes/ms-files.php.
rewrite /files/$ /index.php last;

# For multisite:  Use a caching plugin that creates symlinks to the correct subdirectory structure to get some performance gains.
set $cachetest "$document_root/wp-content/cache/ms-filemap/${host}${uri}";
if ($uri ~ /$) {
	set $cachetest "";
}
if (-f $cachetest) {
	# Rewrites the URI and stops rewrite processing so it doesn't start over and attempt to pass it to the next rule.
	rewrite ^ /wp-content/cache/ms-filemap/${host}${uri} break;
}

if ($uri !~ wp-content/plugins) {
	rewrite /files/(.+)$ /wp-includes/ms-files.php?file=$1 last;
}

# Uncomment one of the lines below for the appropriate caching plugin (if used).
#include global/wordpress-ms-subdir-wp-super-cache.conf;
#include global/wordpress-ms-subdir-w3-total-cache.conf;

# Rewrite multisite '.../wp-.*' and '.../*.php'.
if (!-e $request_filename) {
	rewrite ^/[_0-9a-zA-Z-]+(/wp-.*) $1 last;
	rewrite ^/[_0-9a-zA-Z-]+.*(/wp-admin/.*\.php)$ $1 last;
	rewrite ^/[_0-9a-zA-Z-]+(/.*\.php)$ $1 last;
	rewrite ^.*$ /index.php last;
}
# Pass all .php files onto a php-fpm/php-fcgi server.
location ~ \.php$ {
	root 			html;
	fastcgi_pass	127.0.0.1:9000;
	fastcgi_index	index.php;
	fastcgi_param	SCRIPT_FILENAME /var/www/vhosts/colog.jp$fastcgi_script_name;
	include			fastcgi_params;
}

Thanks.