Good question, the Season 1 episode 2 theme is also one of my favorites, it is actually different from the other themes, that it is a slightly sped up version of the pilot theme. It also sounds kinda nerdy and is 27 seconds long compared to 33 second long regular theme, which btw sounds a bit punk rock to me. I think that that the nerd theme was replaced on the DVD for the normal one.
Yes, Catherine Lloyd Burns was only in the 1 and 2 seasons, but only in a few 1st season theme songs.
And I always did wonder why "And Frankie Muniz" was at the very end, maybe it was building up to his name.