Thank you very much for everyone's input. I found that the problem is with wincache.
I'm not too much of a php guy so it took me a long time to get what stuff means on server event log and php log. The thing that keep popping up is wincache crashing on a daily basis. php-cgi.exe would hang randomly across different sites. After no luck in resolving the crashing issue with PHP upgraded to 5.6, ensuring all windows php drivers are of correct version and Moodle upgraded to 2.9, and after reading about opcache being the only supported cache for PHP 5.6, I uninstalled wincache about a week ago. I was then able to turn off design mode and all the sites remain 'unbroken'.
There hasn't been a single hanging incident for the past week (touch wood). I used to get at least one every 3-4 days. Some pages seem slow but it is overall stable.
If anyone has reference reading about opcache's stat interpretation and performance analysis, i'll appreciate it.
Thanks again everyone.