The problem of unmined towers of blocks in the nether is a known problem. It has something to do with the height map from what I've read.
Apparently there is a work around that involves placing a layer of blocks above the quarry and then removing them. I've tried it and could never get it to work but others have reported success. I just use an arcane bore or IC2 miner in the nether now, it's less of a headache.
Apparently there is a work around that involves placing a layer of blocks above the quarry and then removing them. I've tried it and could never get it to work but others have reported success. I just use an arcane bore or IC2 miner in the nether now, it's less of a headache.