I realize this is a two-year-old topic, but I'm having the same issue. It doesn't matter what I have the rate set to, it only allows about 2 requests per second. This is my config:

in http:
limit_req_zone $binary_remote_addr zone=flood:10m rate=15r/s;

in server location:
limit_req zone=flood;

That should really be all that is necessary, right? I'm using Nginx 1.1.6.