My first thought is timing, but I don't know how you can alter the timing on these.
So my 2nd guess would be burned exhaust valves.
I'd buy the HF leak down tester and run a test to see if the valve are really sealing. You might be able to tell with a compression test, but the leak down tester is about the same price as a compression tester.
My 3rd guess would be a plug that isn't firing and causing raw gas to get into the exhaust where it's ignited by the heat/fire of the others. So if cyl 3 isn't firing, the fuel enters the header and you now have fire in the exhaust.
You can check with a clip on timing light, going from one cyl to another to see if you have fire to the plugs.
You can also check the temp at the header and compare each pipe.
My last guess would be rich backfire, but you should be able to hear that and it would be quite a bit I would guess.
I assume the exhaust isn't wrapped.
If you have a PCIII module, that could be a factor, but I have no idea what params the PCIII has.
Did you do a baffle mod or any other mod?