I can provide a firmware version that uses the rear panel connector instead of the IR port easily enough. But right now, the firmware expects a high going low signal. In other words, what I get out of the IR receiver. So it seems that is the opposite to what is sent out.
I'm experimenting today with inverting the signal in the firmware. That would be the fix. It's opposite of what I originally expected.Update: I have released V1.9 which supports the rear connector. It is located here: http://ps3ir.com/simplemachinesforum/index.php?topic=120.0
The input is ground referenced so you may have to do more than just plug into the flasher output. In my research I found that some flasher outputs actually connect the positive terminal to 12V and switch the negative input to ground.