They explained it completely in the episode. Bascially, the red pill eats away at your body to generate enormous chakra. Its kinda like the Cursed Seal like that. The only problem is, you can't turn it off. Its like a chemical in your body and it just keeps going.
I think this kind of explains that he will be back to his normal size when we next see him as well. From what the other person says it is pretty obvious anyway since that's what all his jutsu's revolve around, but to examine it more logically it would probably be that since the pills are no longer eating at his body (which was what made him thin in the first place) the anidote will likely have to repair some of what it did eat up, thus restoring his original....er....shape. I could be wrong, but that would seem to make sense.