Mark Waid brought back the multiverse with The Kingdom in the late-ish 90s. Since the multiverse was back Grant Morrison wrote JLA: Earth 2 (Since Earth 2 didn't exist, Earth 3 moved up one space, but it recently had to move back, alas what a short lived promotion.)
Then I don't know what happened because the multiverse appeared as late as Kurt Busiek's JLA run, but still DC announced Infinite Crisis and everybody went nuts because it was going to bring the multiverse back... and the whole thing is all kinds of retarded, but that's how DC works. DC is like God, but instead of mysterious, it's retarded.
But in short, that's why Earth 3 appeared before IC.
I used to post as Cissie King in the old SD, but I haven't created an account here yet.