I noticed the same behavior when sending long running requests (>10secs) from chrome with nginx running as a reversy proxy with spdy enabled. What happens is that chrome sends a PING frame, then sends the request, then if it doesn't get a PING reply it will close the connection and resend the request.
You can see the handling of PING failure here:
http://git.chromium.org/gitweb/?p=chromium/src/net.git;a=blob;f=http/http_network_transaction.cc;h=a6d50699c0f1854036772b67c2a0ea1b1e62ae63;hb=HEAD#l1409

The reason chrome isn't getting a PING reply within 10secs is because nginx queues the ping reply and doesn't send it until it gets a response from upstream.
I added a call to ngx_http_spdy_send_output_queue() in ngx_http_spdy_state_ping() to send the PING reply immediately and it solved the problem.

Bahaa Aidi