This might be kind of convoluted, but bear with me. We all know that when Lews Therin and the Hundred Companions sealed the Bore at the end of the War of Power, using a weave of saidin to lock him in. These weaves of saidin were tied to specialized ter'angreal, the cuendillar seals. (They are ter'angreal, says so in the guide). Immediately afterwards, saidin was tainted. What if the weaves binding the Dark One were tainted as well? We all know that the Ways were eventually corrupted by the Taint (although they WERE created after the taint appeared) so whats to say that weaves created while saidin was still clean would not also have been corrupted? The Dark One's counterstroke came right as the Bore was closing, maybe even while the Hundred Companions were weaving the seal. He could very easily have tainted saidin before the completion of his prison, thus tainting the weaves partially or wholly. This would explain why the seals have been slowly breaking. Now here's another question: Why does Lews Therin always rave about breaking the seals? You could argue that he's mad, but he seems odd that the seals should always be singled out for such a reception. What if the seals, the focus for the seal on the Bore, are (were) also the focus for the Taint? This would explain Lews Therin's fanatical desire to break them, as they are subjecting him to continued exposure to the Taint (through Rand). So now that the Taint has been cleansed, one of two things has happened: a., the seals have broken and the Dark One is free once more, b., the remaining seals are whole, the taint has been cleansed from them, and they are now restored to their cuendillar state. On a side note, because the seals are ter'angreal (you can look it up), Elayne or one of the Asha'man could simply use ter'angreal making skills (I think its been agreed that that's Aligning the Matrix ) to align the matrices and restore them to their AOL status.
Roonas says: Well, on the whole I would have to disagree with your statement on the Taint being focused through the cuellindar seals. They were ter'angreal, I agree, but they were stand alone, not needing channeling to be continuously doing their job, they were merely the focus for the weaves placed to seal the bore. If it was the way you describe, someone would have to be channeling non-stop 24/7 to keep the Dark One sealed. I believe the weaves were either tied off, or were merely done once and that was all that was necessary to maintain them. And the fact that they seem to be breaking now is merely a testament to the ramshackle way that they were placed (without Saidar), not because the weave of Saidin used was tainted. Thus, the idea that the taint was being perpetuated through them is false in my eyes. The counter stroke was a one time slam against Saidan that tainted it, and therefore, made the "pool" of Saidan vile, it also does not need to be tended by the Dark One for the taint to be maintained, and is therefore not focused through the seals. As to Lews Therin's rantings on breaking them, I believe that to be more in line with his nihilistic views on destroying or breaking the world again and killing everyone. I do not believe he sees the seals as the focus of the taint.
Also, as a note to your side note about aligning the matrices:I do not think that realigning the matrices on the seals would restore them to their previous status. How would they be replaced into their "places" on the bore once they were "realigned"? It took the Hundred Companions in total to do it, and it was barely done, would remaking the seals really just automatically fix the bore. I do not believe so, but that is another statement for another time.
Call me Tim
This makes sense!