So I found this discrepancy mentioned on Tor.com in a post by Sylas K Barrett . His answer is that Ishamael was never bound...somehow he avoided that fate. Here are his words, which I have to say are pretty compelling:
At the time, I took this as a poetic speech. Believing Ba’alzamon to be the Dark One, I assumed that he meant that, despite being imprisoned, he is not “bound” because he has had the ability to reach out to touch men’s souls, to influence them and their world. He stood figuratively at Lews Therin’s shoulder because it was the Dark One’s taint that caused it. He gave Lews Therin his momentary glimpse of sanity because it was through Shai’tan’s power that the healing was done. But looking at it now, I see that it can be read literally. Elan Morin, also known as Ishamael, the Betrayer of Hope, was actually there. It’s much more simple than I took it all to be.