Maxim, it happened during a flood so that is likely.
The flood has ceased now, and I didn't have time to find the cause during the incident. I am not sure what the conditions are for replicating, it doesn't appear to be limit_req related.
I fixed the issue for us by adding a guard to the access log to not log such cases (since our problems where related to the sheer amount of log entries being written).
Perhaps nginx should not log these cases to the access log, or provide an option for ignoring such cases. Thanks for your infomation, I thought I was going crazy with all the patches I was reading.