So this is going to be a bit of a long post but if i have encounterd this issue no doubt someone else will.

Basically i keep getting read time outs or my web pages take a very long time to load.

My server is Windows 2008 R2 64bit.
Everything runs under either System or Root
1GBPS Connection server is from OVH.co.uk | http://www.ovh.co.uk/dedicated_servers/infra/2014-EG-32.xml

My web application is Joomla 2.5.x
External components i use are com_hwdmediashare and com_kunena.
And i use MySQLi instead of MySQL.

My PHP build is PHP 5.4 (5.4.29) x86 NTS (32bit)
No caching extensions enabled

My MySQL server is 5.6.19 (64bit)
MySQL tables i use are all InnoDB

Sever is Nginx from http://nginx-win.ecsds.eu/ But i was able to replicate this error with the official builds too http://nginx.org/en/download.html

What runs on the server ?
Just Nginx port 80, PHP port 9000-9100, MySQL port 3306.

How i know it is not a MySQL or PHP issue ?
With mysql i enabled slow query logging and i have no queries that are longer than 2 seconds.
With PHP i added into Joomla a time to load page feature it shows me the time to create page was always a second or less. "Time to create page: 0.109 seconds"

Now very often pages take 30 seconds or more to load but yet if i am to access a page through nginx that is not php. (Html or any other static content) it loads instantly all the time.

So how do i serve PHP traffic through Nginx ?
I use FastCGI. (This is what i believe is the culprit.)

Bellow i will link to my Configs and hope someone can help me understand why i am having such a headache and constant read timeouts and downtime of my site(s). Perhaps i have reached my limit with windows and should be using linux :(

PHP.ini Config :
http://pastebin.com/54A3PDwU

MySQL Config : (This was generated by the MySQL installer and the MySQL server runs fine)
http://pastebin.com/DKiWjNqh

Nginx Config :
http://pastebin.com/J3tqnGpJ

Bat Files to run PHP under FastCGI in windows on Nginx (Thanks to itpp2012 for these | http://forum.nginx.org/read.php?2,242895,243597#msg-243597)
multi_run.cmd :
http://pastebin.com/RPikwgnp

runcgi.cmd :
http://pastebin.com/4GYWiEWS

Bare in mind this is a Windows setup not Linux.