I had some similar experience sometimes. Switching to PHP FastCGI (php-fpm) solved it.
I used php5-fpm on the nginx setup, didn't notice a difference, could be a php config issue tho
Is the mysql (I'm assuming that's the database in use) running on socket or tcp?
EDIT: Also, if all else fails, maybe try something like https://blackfire.io/ to see what method is taking too long or if it's a general php slowness.
If you have PHP slowness turning on Zend Opcache might help, I doubt this will fix the "real" problem but it's worth trying. You must be on PHP 5.5 or newer tho.
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