The widespread belief in Randland is that all thirteen Forsaken were imprisoned with the DO when the Bore was sealed by LTT and the Hundred Companions. However, this doesn't seem to be entirely true. Ishamael appears bodily to LTT in the prologue to TEOTW. We know that he must really be there, because he cures LTT's insanity so that he will realize what he has done. From what we know of how channeling works, he could not have done this if he was only some kind of astral projection. That scene takes place shortly after the sealing of the Bore. So, Ishy was not bound right when the DO and the other Forsaken were sealed away.
Many events throughout the Third Age bear Ishy's fingerprints-- the Trolloc Wars (the Trollocs invading Manetheren carried the banner of Ba'alzamon), the creation and continued existence of the Black Ajah, the War of the Hundred Years. Ishy claimed to have influenced Hawkwing [TEOTW: 14, The Stag and Lion, 172]. The Third Age shows a pattern of humanity being kept in a state of disarray. Whenever the people showed signs of becoming unified (Compact of Ten Nations, Hawkwing's empire), some cataclysmic event occurred to split things up again. This worked out too well for the Shadow to be mere coincidence. Clearly, Ishy was active and in control of the Shadow's forces for quite a bit of, if not all of, the Third Age.
Then we have the research of the post-Breaking historian Aran son of Malan son of Senar (presumably an Ogier), as described in [Guide: 5, The Dark One and the Male Forsaken, 52]. This person claims that "there were sightings of, even encounters with, Ishamael after the Bore was sealed, in fact perhaps as much as forty years after." The proposed theory is that "it may have taken some years for Ishamael to be drawn fully into the trap with the other Forsaken.... Ishamael might well be thrown out of the prison holding the others and drawn back again on some regular cycle."
Next, there is the bit in [Guide: 12, The Reign of the High King, 114-5] about Hawkwing's advisor, Jalwin Moerad. Moerad was a mysterious, shady character who insinuated himself into Hawkwing's court in FY 973. Moerad exhibited "frequent long absences, a volatile temper, and a temperament that more than one observer recorded as 'more than half insane.'" Shortly after Moerad became a counselor (late summer FY 974), Hawkwing abruptly turned against the AS (who had previously had a very close relationship with Hawkwing). Moerad was contemptuous of AS. After Hawkwing's death, Moerad advised the three nobles who "came the closest to seizing the whole of Hawkwing's empire," and all three of them met untimely deaths. Finally, "Moerad never aged from the day he first appeared to the day he vanished, abruptly, some forty years later." The personality, the lack of aging, and the forty years business, along with Ishy's claim that he influenced Hawkwing make it clear that Moerad was Ishamael.
Finally and most tellingly, Josh Hildreth points out Moghedien's musings while holding Nynaeve and Elayne in thrall in Tanchico, after Ny and El tell her about the two Forsaken Rand fought in the Stone of Tear:
"So Be'lal is dead. The other sounds like Ishamael, to me. All his pride at being only half-caught, whatever the price - there was less human left in him than any of us when I saw him again; I think he half-believed he was the Great Lord of the Dark - all his three thousand years of machinations, and it comes to an untaught boy hunting him down."
[TSR: 46, Veils, 526]
So, it seems like Ishy was somehow "partially bound." That is, he was not completely locked away in the Dungeon Dimension with the rest of the Forsaken and the DO. He was definitely free right after the sealing of the Bore, and was most likely free at various points during the Third Age. Obviously, he was also the first of the Forsaken to be completely freed of the seals, by a long shot.