This is supposition. We know the Seals weren't perfect, but we aren't told why. Rand/LTT's best guess so far is that it failed because only Saidin was used, but RJ said that if both halves were used, both would have been tainted.

There was a distinct possibility that the only way to Seal the Bore for good would be to allow both powers to be Tainted (and perhaps the Taint would fade away by the next cycle of the Wheel - even after just 3000 years it seems to be much less virulent than it was during the Breaking.