WordPress 4.5.2 Daily Auto Update Fails

Hi,

I have my own production low volume virtualized server running PHP 5.6, Mariadb, Nginx 1.9+. Several WP sites are stuck at 4.5 and cannot be updated to 4.5.2. What happens is: clicking the “please update button” in the admin area launches the update routine, and states that it is successful. However, at its conclusion, the site comes right back to v 4.5 (even though I get an email stating that the site has been updated to 4.5.2). In fact, the auto update happens a couple times per day, all with the same problem.

So, here’s what I’ve done to track down the problem on one site as a test:
1) Permissions: User and group set the same
chown -R nginx:nginx /var/www/html/somesite.com/
wp-config = 440, directories = 750, files = 640
2) Disabled all plugins
3) Using WP 2016 default theme
4) Optimized and removed orphans from the database
5) Restarted Nginx
6) Tried removing _site_transient_update_core as some have suggested.
7) Removed and reinstalled latest version of WP via FTP
Nothing works. Wondering if this a Nginx issue.

Below are two code sections for you to inspect, to see if I’m missing something:
a) wp-config (redacted as appropriate, left out the db and salted stuff)

/** WordPress Database Table prefix **/
$table_prefix  = 'someprefix_';

/** For developers: WordPress debugging mode **/
define('WP_DEBUG', false);

/** Absolute path to the WordPress directory. **/
if ( !defined('ABSPATH') )
	define('ABSPATH', dirname(__FILE__) . '/');

/** Change Path to Uploads **/
define( 'UPLOADS', 'assets' );

/** Location to cache file
define( 'RT_WP_NGINX_HELPER_CACHE_PATH','/dev/shm/nginx/' );
**/

/** SSL Parameters
define( 'FORCE_SSL_ADMIN', true );
define( 'WP_HTTP_BLOCK_EXTERNAL', false );
**/

/** Increase Memory Available from PHP **/
define( 'WP_MAX_MEMORY_LIMIT', '256M' );

/** Sets up WordPress vars and included files. */
require_once(ABSPATH . 'wp-settings.php');

b) nginx conf file (I put all the includes together here for convenience).

# For more information on configuration, see:
#   * Official English Documentation: https://nginx.org/en/docs/
#   * Official Russian Documentation: https://nginx.org/ru/docs/

user  nginx;
worker_processes  4;

error_log   /var/log/nginx/error.log;

pid        /run/nginx.pid;

events {
    worker_connections  1024;
}

http {

    # Fast CGI Caching
    # fastcgi_cache_path /dev/shm/nginx levels=1:2 keys_zone=stupidfast:16m max_size=1024m inactive=60m;
    # fastcgi_cache_key "$scheme$request_method$host$request_uri";
    #fastcgi_cache_use_stale error timeout invalid_header http_500;

    add_header rt-Fastcgi-Cache $upstream_cache_status;

    charset UTF-8;

    # hide some server information
    server_tokens off;
    server_name_in_redirect off;

    include       /etc/nginx/mime.types;

    default_type  application/octet-stream;

    log_format  main  '$remote_addr - $remote_user [$time_local] "$request" '
                      '$status $body_bytes_sent "$http_referer" '
                      '"$http_user_agent" "$http_x_forwarded_for"';

    # access_log  /var/log/nginx/access.log  main;
    access_log off;

    sendfile        on;
    #tcp_nopush      on;
    tcp_nodelay     on;

    client_header_buffer_size 1k;
    client_max_body_size 20m;
    client_body_buffer_size 128K;
    large_client_header_buffers 4 16k;

    client_body_timeout 12;
    client_header_timeout 12;
    keepalive_timeout 10s;
    send_timeout 10;
    types_hash_max_size 2048;
    server_names_hash_bucket_size 64;

    # Enable Gzip compressed.
    gzip on;

    # Compression level (1-9).
    # 5 is a perfect compromise between size and cpu usage, offering about
    # 75% reduction for most ascii files (almost identical to level 9).
    gzip_comp_level    6;

    # Don't compress anything that's already small and unlikely to shrink much
    # if at all (the default is 20 bytes, which is bad as that usually leads to
    # larger files after gzipping).
    gzip_min_length    256;

    # Compress data even for clients that are connecting to us via proxies,
    # identified by the "Via" header (required for CloudFront).
    gzip_proxied       any;

    gzip_buffers 16 8k;

    # Tell proxies to cache both the gzipped and regular version of a resource
    # whenever the client's Accept-Encoding capabilities header varies;
    # Avoids the issue where a non-gzip capable client (which is extremely rare
    # today) would display gibberish if their proxy gave them the gzipped version.
    gzip_vary          on;

    # Compress all output labeled with one of the following MIME-types.
    gzip_types
    application/atom+xml
    application/font-otf
    application/font-ttf
    application/json
    application/ld+json
    application/manifest+json
    application/rss+xml
    application/vnd.geo+json
    application/vnd.ms-fontobject
    application/x-font-ttf
    application/x-javascript
    application/x-web-app-manifest+json
    application/xhtml+xml
    application/xml
    font/opentype
    image/bmp
    image/svg+xml
    image/x-icon
    text/cache-manifest
    text/css
    text/javascript
    text/xml
    text/plain
    text/vcard
    text/vnd.rim.location.xloc
    text/vtt
    text/x-component
    text/x-cross-domain-policy;
    # text/html is always compressed by HttpGzipModule

    server {
    listen [::]:80;
    listen 80;
    server_name somesite.com www.somesite.com;

    root    /var/www/html/somesite.com/wwwroot;

    access_log  /var/log/nginx/somesite.access.log main;
    error_log   /var/log/nginx/somesite.error.log warn;

    # -- Error Pages
    # show "Not Found" 404 errors in place of "Forbidden" 403 errors,
    # because forbidden errors allow attackers potential insight into your server's layout and contents
    error_page 403 = 404;

    error_page 404      /404.html;
    location = /40x.html {
    }

    error_page 500 502 503 504  /50x.html;
    location = /50x.html {
    }

    # -- Security and Location
    location = /robots.txt  { allow all; access_log off; log_not_found off; }
	location = /favicon.ico { access_log off; log_not_found off; }

	# prevent browsing hidden files (beginning with a period) from being served
	location ~ /\.          { access_log off; log_not_found off; deny all; }

    # prevent access to any files starting with a $ (usually temp files)
    location ~ ~$ { access_log off; log_not_found off; deny all; }

    # prevent browsing to certain wordpress files
    location ~* /wp-includes/.*.php$ { deny all; access_log off; log_not_found off; }
    location ~* /wp-content/.*.php$ { deny all; access_log off; log_not_found off; }
    location ~* /(?:uploads|files)/.*.php$ { deny all; access_log off; log_not_found off; }
    location = /xmlrpc.php { deny all; access_log off; log_not_found off; }

    # add trailing slash to */wp-admin requests so the admin interface works correctly
    rewrite /wp-admin$ $scheme://$host$uri/ permanent;

    # -- Prevent Caching of Static Resources
    set $no_cache 0;
    if ($request_method = POST) {
        set $no_cache 1;
    }
    if ($query_string != "") {
        set $no_cache 1;
    }
    if ($request_uri ~* "(/wp-admin/|/xmlrpc.php|/wp-(app|cron|login|register|mail).php|wp-.*.php|/feed/|index.php|wp-comments-popup.php|wp-links-opml.php|wp-locations.php|sitemap(_index)?.xml|[a-z0-9_-]+-sitemap([0-9]+)?.xml)") {
        set $no_cache 1;
    }
    if ($http_cookie ~* "comment_author|wordpress_[a-f0-9]+|wp-postpass|wordpress_no_cache|wordpress_logged_in") {
        set $no_cache 1;
    }

    # -- Caching Controls
    # keep images, CSS and other static files around in browser cache for as long as possible, to cut down on server load
    location ~* .(ogg|ogv|svg|svgz|eot|otf|woff|mp4|ttf|css|rss|atom|js|jpg|jpeg|gif|png|ico|zip|tgz|gz|rar|bz2|doc|xls|exe|ppt|tar|mid|midi|wav|bmp|rtf)$ {
        access_log off;
        log_not_found off;
        expires max; # 360d;
		add_header Pragma public;
		add_header Cache-Control "public, must-revalidate, proxy-revalidate";
	}

    #location ~* .(php|html)$ {
       #access_log off;
       #log_not_found off;
       #add_header Pragma public;
       #add_header Cache-Control "public";
       #expires 14d;
    #}

    # -- General Directives
    location / {
        # First attempt to serve request as file, then as directory, then fall back to index.html
        # This is cool because no php is touched for static content.
        # include the "?$args" part so non-default permalinks doesn't break when using query string
        # if you're just using wordpress and don't want extra rewrites
        # then replace the word @rewrites with /index.php
        # try_files $uri $uri/ @rewrites;
        index index.php index.html index.htm;
        try_files $uri $uri/ /index.html /index.php?$args;
    }

    location @rewrites {
		# Can put some of your own rewrite rules in here
		# for example rewrite ^/~(.*)/(.*)/? /users/$1/$2 last;
		# If nothing matches we'll just send it to /index.php
		rewrite ^ /index.php last;
	}

    location ~ \.php$ { 

        #fastcgi_pass_header Set-Cookie;
        #fastcgi_pass_header Cookie;
        #fastcgi_ignore_headers Cache-Control Expires Set-Cookie;
        fastcgi_index index.php;
        fastcgi_param SCRIPT_FILENAME $document_root$fastcgi_script_name;
        fastcgi_split_path_info ^(.+\.php)(/.+)$;
        fastcgi_param  PATH_INFO $fastcgi_path_info;
        fastcgi_param  PATH_TRANSLATED    $document_root$fastcgi_path_info;
        fastcgi_intercept_errors on;
        fastcgi_pass unix:/var/run/php5.6-fpm/php5.6-fpm.sock;

        fastcgi_param  GATEWAY_INTERFACE    CGI/1.1;
        fastcgi_param  SERVER_SOFTWARE      nginx/$nginx_version;

        fastcgi_param  QUERY_STRING         $query_string;
        fastcgi_param  REQUEST_METHOD       $request_method;
        fastcgi_param  CONTENT_TYPE         $content_type;
        fastcgi_param  CONTENT_LENGTH       $content_length;
        fastcgi_param  SCRIPT_NAME          $fastcgi_script_name;
        fastcgi_param  REQUEST_URI          $request_uri;
        fastcgi_param  DOCUMENT_URI         $document_uri;
        fastcgi_param  DOCUMENT_ROOT        $document_root;
        fastcgi_param  SERVER_PROTOCOL      $server_protocol;
        fastcgi_param  HTTPS                $https if_not_empty;

        fastcgi_param  REMOTE_ADDR          $remote_addr;
        fastcgi_param  REMOTE_PORT          $remote_port;
        fastcgi_param  SERVER_ADDR          $server_addr;
        fastcgi_param  SERVER_PORT          $server_port;
        fastcgi_param  SERVER_NAME          $server_name;

        # PHP only, required if PHP was built with --enable-force-cgi-redirect
        fastcgi_param  REDIRECT_STATUS      200;

        # Caching Bypasses
        #fastcgi_no_cache $no_cache;
        #fastcgi_cache_bypass $no_cache;
        #fastcgi_cache stupidfast;
        #fastcgi_cache_key $server_name|$request_uri; 

        # Caching Expiration and Headers
        #fastcgi_cache_valid 404 60m;
        #fastcgi_cache_valid 200 60m;
        #fastcgi_max_temp_file_size 4m;
        #fastcgi_max_temp_file_size 0;
        #fastcgi_cache_use_stale updating;
        #fastcgi_cache_valid   200 302  1h;
        #fastcgi_cache_valid   301 1h;
        #fastcgi_cache_valid   any 1h;
        #fastcgi_cache_min_uses  2;

        fastcgi_buffer_size 4K;
        #fastcgi_buffer_size 128K;
        fastcgi_buffers 64 4k;
        #fastcgi_buffers 4 256k;
        #fastcgi_ignore_client_abort off;
        #fastcgi_connect_timeout 60;
        #fastcgi_send_timeout 90;
        #fastcgi_read_timeout 90;
        #fastcgi_busy_buffers_size 256k;
        #fastcgi_temp_file_write_size 256k;

        #fastcgi_pass localhost:9000; 

        fastcgi_param  WP_NGINX_CONFIG      done;
    }
}

}