The same way you put the other codes in. Double click the button, select actions tab, add IR code, and then view/edit IR. Put the code in the window (copy/paste or type) and test it out. I think you are already doing this though? IPronto will not stop editing the code, it is putting it in to its format as far as I know. See if the RAW code works, and what happens when you re-encode it.

Put up two of the Pronto Pro codes and I'll see what I get and post it back.

If anyone else knows more please correct me.