You should check that all the different limits in both PHP and nginx are properly configured to handle file uploads. This answer in serverfault.com, while not Magento specific, lists the configuration directives that you might want to check in php.ini and nginx conf: http://serverfault.com/questions/611239/increase-php-fpms-max-upload-post-size
If this doesn't help, I suggest looking at your php error log and nginx error log for relevant errors and posting them here.
Shahar Evron
CTO,
Shoppimon - Website Monitoring, Made for Magento