Alright, now we're getting somewhere.
Found more of the Chicago Muni Code. Seemed odd they would have one that didn't include traffic signals.
9-08-030
Whenever flashing red or yellow signal indications are in place, the signals shall indicate and apply to drivers of vehicles as follows:
(a) Flashing Red Indication. When a red signal is illuminated with rapid intermittent flashes, the operator of any vehicle shall stop before entering the nearest crosswalk at an intersection or at a stop line when marked, or, if none, then before entering the intersection, and the right to proceed shall be subject to the rules applicable after making a stop at a stop sign.
(b) Flashing Yellow Indication. When a yellow signal is illuminated with rapid intermittent flashes, the operator of any vehicle may proceed through the intersection or past such signal only with caution.
Here's a link to the city's revenue dept online. There may be some links on there that are of use to you:
http://egov.cityofchicago.org/city/webportal/portalEntityHomeAction.do?entityName=Revenue&entityNameEnumValue=36
or
http://tinyurl.com/ktwtqz
Chicago muni code [traffic code is in section 9]:
http://www.amlegal.com/nxt/gateway.dll/Illinois/chicago_il/municipalcodeofchicago?f=templates $fn=default.htm$3.0$vid=amlegal:chicago_il
or
http://tinyurl.com/234zws
9-102 is the red light traffic camera section
9-8 is the traffic signals section
BOTTOM LINE: I've searched using different terms, and I've read entire sections that would seem to logically potentially contain a reference to a dual flashing amber light. I can't find any reference anywhere in the Chicago muni code for that. I'm still puzzled about that one.
I think that either there is something about such a signal in some code elsewhere (such as state law) or not at all; or they are saying the light turned red while your vehicle was passing through the intersection. I would call the revenue department, ask to speak to someone who can answer questions about red light cameras, and ask specifically what law it was that was violated. Ask them about the double flashing amber light, what the hell it means, and what code or statute defines what answer they give you. If they are just saying flat-out that the vehicle passed through the intersection when the light turned red, you may be SOL unless you're willing to go back for a hearing.
HOWEVER, some places allow hearings where you can appear by telephone. You may not feel like that is much of a hearing, but it's better than having no say or spending hundreds of $$$ to fly back and fight it in person, isn't it?
Also, I found some discussions of these in a couple places. I haven't had time to read through all of this, so there could be some nuggets in there, or they could all be crap. A few words of caution.
1. Amateur lawyers or people who say what the law is or ought to be but who aren't lawyers are frequently wrong in their interpretations and opinions on these kind of sites.
2. Some arguments may have been offered in court and rejected. Judges face this repeat "business" fairly regularly in some courts. It's sort of like the guys who argue the constitution prevents the federal government from taxing us. They make these arguments and pass them around. They never work. If they did, they'd be all over TV, newspapers, etc.
3. Um....crap, I forget what the third thing was...
I'm including these links just in case there is anything in there that has actually worked in court or in a case.
http://www.yelp.com/topic/chicago-do-chicagos-red-light-traffic-cameras-violate-due-process
http://www.chicago-red-light-ticket-defense.com/