The Secret Episodes refer to Heavenward and Hades, which were not broadcast during the original 2003 airing of the show in Japan.
This might be explained by the interview with ABe and Ueda included on the DVD release(s) of the series - supposedly, Konaka was about one and a half to two months late in finalizing the scripts for the 'last few episodes', though direct reference is only made to the final two.
Both of these episodes were included in the English airing of the series in 2007, however.