another iterative release of the auto-normaliser tool for you to try :)

http://abscnc.sourceforge.net/will/wwtools/normaliser1.2.zip

This is the normals on the APC from TS:

<img src="http://abscnc.sourceforge.net/will/wwtools/apc_ts_orig.gif">

and this is the same voxel after going through the auto-normaliser:

<img src="http://abscnc.sourceforge.net/will/wwtools/apc_ts2_1.gif">

Using flyby's normals

might still be some bugs. Can't cope well with those voxels that some people put under sloping faces, so you'll have to do that those manually. It doesn't remove them or anything :D