Is there an nginx queue that isn't logged via $response_time

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We have a setup that looks like this:

nginx->haproxy->app servers

We are terminating SSL with nginx and it sits in front of everything. During
our peak load times, we are experiencing about a 2x performance hit.
Requests that would normally take 400 ms are taking 800ms. It's taking
longer for the entire Internet.

The problem is, I have absolutely no sign of any slowdowns in my logs and
graphs. New Relic shows all the app servers are responding correctly with no
change in speed. Nginx and haproxy show nothing in their logs about requests
slowing down, but we are slowing down at end users. Despite nginx showing
that a particular request I tracked is taking 17ms ($response_time) through
the entire stack, it took 1.5 seconds to curl it during peak load last
week.

So, that leaves me with two options: 
1) Network issues - I have more than enough pipe left according to graphs
from the router. I'm only using 400 Mbps out of the 1 Gbps port and there
are no errors in ifconfig or on the switch or routers. However, SoftLayer
manages this gear, so I can't verify this personally.

2) nginx is holding up the request and either not logging it or I'm not
logging the right thing. Is it possible that requests are being queued up
because workers are busier and they're not getting acted on as quickly? If
this is in fact happening, what can I log in nginx other than
$response_time, since that is showing no slowdown at all. And, if this is
possible that requests are actually taking longer than $response_time is
indicating, how do I go about tweaking the config to speed things up?

Posted at Nginx Forum: http://forum.nginx.org/read.php?2,243170,243170#msg-243170