First off Both Amon and Mako/Bolin had there families killed by a fire Bender. So of course my theory is that the incidents are one in the same.
Amon probably thought his sons were killed after being near burned to death. And Mako didn't think his father survived that so he went off with Bolin somewhere. So none of them know about each other being family.
Now you might say that when he saw Bolin in episode 3 he didn't recognise him. Maybe that is because he has gotten so involved in his work and so driven by it that he has forgotten their appearances and thought of them as common benders. Or he does in fact know that they are his sons and doesn't know how to break it to them or simply hasn't had the time.
Now the stories they told were slightly different, but Mako was a child so his memory of the event could look very different then what it actually was.
Second if you pause this video at 5 seconds in, you will see Amon's Eye:
http://www.nick.com/videos/clip/legend-of-korra-finale-extended-saturday-june-23rd-N14915-07.html
Here is a clearer version:
Look familiar?
You see their eyes are identical. Now Bolin has green eyes but that probably is because his genes are more like his mothers.
My third point is this picture:
It's from the season finale. It seems that Mako might have had a realization (about Amon) and is confused. As well as seeing what his father is doing to his love must be very heartbreaking.
So in conclusion this is a lot of proof to support my theory. This is all I got so far but I will find more. And if you have some, feel free to post them in the comments below.
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Burning Spies is one of my Specialties!