takuword

更に詳しい情報が出てきました。

jQuery version: 1.10.2

CLIENT_ID: (hidden)
BLOG_TOKEN: (hidden)
MASTER_USER: (hidden)
CERT: 0
TIME_DIFF: 0
VERSION: 2.5:1379729025
OLD_VERSION: 2.4.2:1378376242
PUBLIC: (hidden)
USER_ID: (hidden)
USER_TOKEN: (hidden)
PHP_VERSION: 5.4.9-4ubuntu2.3
WORDPRESS_VERSION: 3.6.1
JETPACK__VERSION: 2.5
JETPACK__PLUGIN_DIR: (hidden)/wp-content/plugins/jetpack/
SITE_URL: http://jre655.com
HOME_URL: http://jre655.com

TEST RESULTS:

HTTP: PASS
HTTPS: PASS
IDENTITY_CRISIS: PASS
SELF: FAIL

RAW TEST RESULTS:

HTTP
Array
(
    [headers] => Array
        (
            [server] => nginx
            [date] => Sat, 21 Sep 2013 02:23:01 GMT
            [content-type] => text/plain;charset=utf-8
            [connection] => close
            [vary] => Cookie
            [x-pingback] => http://jetpack.wordpress.com/xmlrpc.php
            [expires] => Wed, 11 Jan 1984 05:00:00 GMT
            [cache-control] => no-cache, must-revalidate, max-age=60
            [pragma] => no-cache
            [x-hacker] => Jetpack Test
        )

    [body] => OK
    [response] => Array
        (
            [code] => 200
            [message] => OK
        )

    [cookies] => Array
        (
        )

    [filename] =>
)

HTTPS
Array
(
    [headers] => Array
        (
            [server] => nginx
            [date] => Sat, 21 Sep 2013 02:23:02 GMT
            [content-type] => text/plain;charset=utf-8
            [connection] => close
            [vary] => Cookie
            [x-pingback] => http://jetpack.wordpress.com/xmlrpc.php
            [expires] => Wed, 11 Jan 1984 05:00:00 GMT
            [cache-control] => no-cache, must-revalidate, max-age=60
            [pragma] => no-cache
            [x-hacker] => Jetpack Test
        )

    [body] => OK
    [response] => Array
        (
            [code] => 200
            [message] => OK
        )

    [cookies] => Array
        (
        )

    [filename] =>
)

IDENTITY_CRISIS
PASS

SELF
Array
(
    [headers] => Array
        (
            [server] => nginx
            [date] => Sat, 21 Sep 2013 02:23:07 GMT
            [content-type] => text/plain;charset=utf-8
            [connection] => close
            [x-pingback] => http://jetpack.wordpress.com/xmlrpc.php
            [expires] => Wed, 11 Jan 1984 05:00:00 GMT
            [cache-control] => no-cache, must-revalidate, max-age=60
            [pragma] => no-cache
            [x-hacker] => Jetpack Test
        )

    [body] => {"error":"Communication error","error_description":"We were unable to make an XML-RPC request to your website. Please make sure that XML-RPC is turned on and that Jetpack is installed, activated and connected with your WordPress.com account. If the error persists, try disconnecting and connecting Jetpack again."}
    [response] => Array
        (
            [code] => 400
            [message] => Bad Request
        )

    [cookies] => Array
        (
        )

    [filename] =>
)

追加情報です。
JetPackのデバッグセンターでテストすると以下の様にエラーになってしまいます。

SELF:
	Array
(
    [headers] => Array
        (
            [server] => nginx
            [date] => Wed, 11 Sep 2013 10:09:58 GMT
            [content-type] => text/plain;charset=utf-8
            [connection] => close
            [x-pingback] => http://jetpack.wordpress.com/xmlrpc.php
            [expires] => Wed, 11 Jan 1984 05:00:00 GMT
            [cache-control] => no-cache, must-revalidate, max-age=60
            [pragma] => no-cache
            [x-hacker] => Jetpack Test
        )

    [body] => {"error":"Communication error","error_description":"We were unable to make an XML-RPC request to your website. Please make sure that XML-RPC is turned on and that Jetpack is installed, activated and connected with your WordPress.com account. If the error persists, try disconnecting and connecting Jetpack again."}
    [response] => Array
        (
            [code] => 400
            [message] => Bad Request
        )

    [cookies] => Array
        (
        )

    [filename] =>
)

ですが、こちらにあるプラグインを使用してテストするといずれも200で成功となります。

Site info

SITE_URL: http://jre655.com
HOME_URL: http://jre655.com
TEST: HTTP Connection

Array
(
    [headers] => Array
        (
            [server] => nginx
            [date] => Wed, 11 Sep 2013 10:11:59 GMT
            [content-type] => text/plain;charset=utf-8
            [connection] => close
            [vary] => Cookie
            [x-pingback] => http://jetpack.wordpress.com/xmlrpc.php
            [expires] => Wed, 11 Jan 1984 05:00:00 GMT
            [cache-control] => no-cache, must-revalidate, max-age=60
            [pragma] => no-cache
            [x-hacker] => Jetpack Test
        )

    [body] => OK
    [response] => Array
        (
            [code] => 200
            [message] => OK
        )

    [cookies] => Array
        (
        )

    [filename] =>
)
TEST: HTTPS Connection

Array
(
    [headers] => Array
        (
            [server] => nginx
            [date] => Wed, 11 Sep 2013 10:12:00 GMT
            [content-type] => text/plain;charset=utf-8
            [connection] => close
            [vary] => Cookie
            [x-pingback] => http://jetpack.wordpress.com/xmlrpc.php
            [expires] => Wed, 11 Jan 1984 05:00:00 GMT
            [cache-control] => no-cache, must-revalidate, max-age=60
            [pragma] => no-cache
            [x-hacker] => Jetpack Test
        )

    [body] => OK
    [response] => Array
        (
            [code] => 200
            [message] => OK
        )

    [cookies] => Array
        (
        )

    [filename] =>
)
TEST: Self Connection

Array
(
    [headers] => Array
        (
            [server] => nginx
            [date] => Wed, 11 Sep 2013 10:12:01 GMT
            [content-type] => text/plain;charset=UTF-8
            [connection] => close
            [x-cached] => Wed, 11 Sep 2013 10:12:00 GMT
        )

    [body] => XML-RPC server accepts POST requests only.
    [response] => Array
        (
            [code] => 200
            [message] => OK
        )

    [cookies] => Array
        (
        )

    [filename] =>
)

さらに、画像の配置もおかしいです。
こちらから確認できます。

わかりました、試してみます。

アクセスログに以下のものがありました
76.74.248.176, 108.162.221.26 – – [31/Aug/2013:14:21:08 +0900] “POST /xmlrpc.php?for=jetpack&rand=2057882416 HTTP/1.0” 200 448 “-” “The Incutio XML-RPC PHP Library”

76.74.248.176, 108.162.221.26 – – [31/Aug/2013:14:21:09 +0900] “POST /xmlrpc.php?for=jetpack&token=iDe%24R%28OR2%5E0BQlZY%2AS3ctqfsa%2AgG%2A%29wL%3A1%3A1&timestamp=13779264 69&nonce=YK4v0Ko9DT&body-hash=pdst%2B%2B8gjpsEsdzTGdS19%2BYN3g4%3D&signature=%2BYfstyf hAnk7xVoUClOnJQJCLWg%3D HTTP/1.0” 200 444 “-” “Jetpack by WordPress.com”
これがなにかヒントになればよいのですが…

止めてからもダメでした。
あと、連携の承諾後に、一回502 Bad Gatewayが出て、リロードすると正常に連携されています、が出ます。

NginxおよびPHP-FPM,Perconaの設定はAmimotoのGitリポジトリをベースにして作ってあります。なので、特に問題はないと思われます。
モジュールで問題になるようなものは入ってません(とは断定できませんが…)
一応これらが原因とは思いませんが念の為にこちらにPHPモジュールをリストアップしておきます。

dpkg -l | grep php
ii  libphp-adodb                              5.15-1                               all          ADOdb database abstraction layer for PHP
ii  php-gettext                               1.0.11-1                             all          read gettext MO files directly, without requiring anything other than PHP
ii  php-pear                                  5.4.9-4ubuntu2.2                     all          PEAR - PHP Extension and Application Repository
ii  php5                                      5.4.9-4ubuntu2.2                     all          server-side, HTML-embedded scripting language (metapackage)
ii  php5-adodb                                5.04-7build1                         amd64        Extension optimising the ADOdb database abstraction library
ii  php5-cli                                  5.4.9-4ubuntu2.2                     amd64        command-line interpreter for the php5 scripting language
ii  php5-common                               5.4.9-4ubuntu2.2                     amd64        Common files for packages built from the php5 source
ii  php5-curl                                 5.4.9-4ubuntu2.2                     amd64        CURL module for php5
ii  php5-dev                                  5.4.9-4ubuntu2.2                     amd64        Files for PHP5 module development
ii  php5-fpm                                  5.4.9-4ubuntu2.2                     amd64        server-side, HTML-embedded scripting language (FPM-CGI binary)
ii  php5-gd                                   5.4.9-4ubuntu2.2                     amd64        GD module for php5
ii  php5-imagick                              3.1.0~rc1-1build2                    amd64        ImageMagick module for php5
ii  php5-intl                                 5.4.9-4ubuntu2.2                     amd64        internationalisation module for php5
ii  php5-mcrypt                               5.4.6-0ubuntu1                       amd64        MCrypt module for php5
ii  php5-memcache                             3.0.7-2                              amd64        memcache extension module for PHP5
ii  php5-mysql                                5.4.9-4ubuntu2.2                     amd64        MySQL module for php5
ii  php5-snmp                                 5.4.9-4ubuntu2.2                     amd64        SNMP module for php5
ii  php5-xmlrpc                               5.4.9-4ubuntu2.2                     amd64        XML-RPC module for php5

nginx -V
nginx version: nginx/1.4.2
TLS SNI support enabled
configure arguments: --prefix=/etc/nginx --sbin-path=/usr/sbin/nginx --conf-path=/etc/nginx/nginx.conf --error-log-path=/var/log/nginx/error.log --http-log-path=/var/log/nginx/access.log --pid-path=/var/run/nginx.pid --lock-path=/var/run/nginx.lock --http-client-body-temp-path=/var/cache/nginx/client_temp --http-proxy-temp-path=/var/cache/nginx/proxy_temp --http-fastcgi-temp-path=/var/cache/nginx/fastcgi_temp --http-uwsgi-temp-path=/var/cache/nginx/uwsgi_temp --http-scgi-temp-path=/var/cache/nginx/scgi_temp --user=nginx --group=nginx --with-http_realip_module --with-http_addition_module --with-http_sub_module --with-http_gzip_static_module --with-http_stub_status_module --with-http_ssl_module --add-module=/home/(user)/deb/nginx-1.4.1/debian/module/ngx_cache_purge-2.1 -with-http_spdy_module

megumiteam/amimoto|Github
そして、同サーバーで管理している他のサイト(内容がひどいメモサイト、こちらはCloudFlareをかましてません)でもエラーでした。となると、CloudFlareの問題ではないと思われます。