Here's another theory that was posted somewhere.

Remember that when an avatar dies, a new one is born. Remember how Aang was killed by a lightning bender and then revived by Katara? So, the theory is...when Aang first died, Amon was born as the new avatar, however, since Aang was revived again, Amon lost the avatar bending powers but still kept the ability to take away bending. Then, once Aang died years later, Korra was born and once again a new avatar was born.

This theory sounds legit, however, that would mean Amon is a lot older than he may look.