*Edit* Replacing the quarry and chunkloading the area has made no difference, it's still skipping over the chunks that it skipped the first time.
But the three chunks that have been excavated were covered in tainted soil as well, and it's dug up all that.A quarry will not recognise most custom blocks and from what I can make out that's tainted soil on top of the netherrack which a quarry most likely wont dig.