Пересобрали nginx вот так:
nginx version: nginx/1.8.0
built by gcc 4.2.1 20070719 [FreeBSD]
built with OpenSSL 0.9.8q 2 Dec 2010
TLS SNI support enabled
configure arguments: --prefix=/usr/local/etc/nginx --with-cc-opt='-I /usr/local/include' --with-ld-opt='-L /usr/local/lib' --conf-path=/usr/local/etc/nginx/nginx.conf --sbin-path=/usr/local/sbin/nginx --pid-path=/var/run/nginx.pid --error-log-path=/var/log/nginx-error.log --user=www --group=www --with-file-aio --http-client-body-temp-path=/var/tmp/nginx/client_body_temp --http-fastcgi-temp-path=/var/tmp/nginx/fastcgi_temp --http-proxy-temp-path=/var/tmp/nginx/proxy_temp --http-scgi-temp-path=/var/tmp/nginx/scgi_temp --http-uwsgi-temp-path=/var/tmp/nginx/uwsgi_temp --http-log-path=/var/log/nginx-access.log --with-http_geoip_module --with-pcre --with-http_ssl_module --with-debug

Оставили только то, без чего никак не обойтись. Кастомных патчей нет.

Картина при этом не изменилась совершенно. Видим абсолютно то же поведение:
2015/07/16 10:35:28 [debug] 86051#0: *496647 http process request line
2015/07/16 10:35:28 [debug] 86051#0: *496647 http request line: "POST /?id=10046 HTTP/1.1"
2015/07/16 10:35:28 [debug] 86051#0: *496647 http uri: "/"
2015/07/16 10:35:28 [debug] 86051#0: *496647 http args: "id=10046"
2015/07/16 10:35:28 [debug] 86051#0: *496647 http exten: ""
2015/07/16 10:35:28 [debug] 86051#0: *496647 http process request header line
2015/07/16 10:35:28 [debug] 86051#0: *496647 http header: "Content-Type: application/json; charset=utf-8"
2015/07/16 10:35:28 [debug] 86051#0: *496647 http header: "x-openrtb-version: 2.0"
2015/07/16 10:35:28 [debug] 86051#0: *496647 http header: "Content-Length: 1151"
2015/07/16 10:35:28 [debug] 86051#0: *496647 post event 000000080C20B600
2015/07/16 10:35:28 [debug] 86051#0: *496647 delete posted event 000000080C20B600
2015/07/16 10:35:28 [debug] 86051#0: *496647 http process request line
2015/07/16 10:35:28 [debug] 86051#0: *496647 http finalize request: 400, "?" a:1, c:1
2015/07/16 10:35:28 [debug] 86051#0: *496647 http special response: 400, "?"
2015/07/16 10:35:28 [debug] 86051#0: *496647 http set discard body
2015/07/16 10:35:28 [debug] 86051#0: *496647 charset: "" > "utf-8"