At the end of last week I noticed a problem on one of my medium AWS instances where Nginx always returns a HTTP 499 response if a request takes more than 60 seconds. The pa
You need to find in which place problem live. I dont' know exact answer, but just let's try to find it.
We have here 3 elements: nginx, php-fpm, php. As you told, same php settings under apache is ok. Does it's same no same setup? Did you try apache instead of nginx on same OS/host/etc.?
If we will see, that php is not suspect, then we have two suspects: nginx & php-fpm.
To exclude nginx: try to setup same "system" on ruby. See https://github.com/garex/puppet-module-nginx to get idea to install simplest ruby setup. Or use google (may be it will be even better).
My main suspect here is php-fpm.
Try to play with these settings: