I was confused by that too when I first watched it. I think it was probably for marketing purposes. At that point in time Charmander was probably far more popular than Charizard, so since those episodes weren't really in the story-line of the show much they decided to bring Charmander back?
That's just a theory of course, and could be dead wrong. *Shrugs*
omg I know right, I had wondered that for many years, it was so confusing! lol that was weird....but cool.