Could you remove these parts of Minecraft caves?
It looks very ugly.
http://dl.dropbox.com/u/53753604/temp/2012-03-31_22.31.56.png

Blocks to remove:
5, 54, 66, 85

What you are seeing is actually an artifact of how Minecraft and Bukkit generate terrain. Structures are the last thing to be added to a chunk, even after custom block populators like Giant Caves. Essentially, when Giant Caves runs, the mine shafts you are seeing don't exist yet. Giant Caves sets all blocks inside the cave to air.

The solution is to increase the value of minY in your config to a layer above the mine shafts.