Section 1034:

History: the json file was created a while ago with an older
version of ImageEditor and with an unmasked image of section
1034. See image dirty_background.png along the junction of 
the moved piece (Polygon 4, layer 4).

Image:
- pm1034o.png : this is the new masked section for input.

Project files:
- pm1034o.json : created from unmasked image (dirty background).
                 Layers contains RGB+A.
- new1034o.json : loaded pm1034o.json and saved with binarymask=true
                  (file size is much smaller!!!)
- test1034o.json : edited (vim) pm1034o.json and deleted all layers
                   and transformations. Kept only the polygons.

-rw-r--r--. 1 clepage clepage   96325 Jun  2 10:04 new1034o.json
-rw-r--r--. 1 clepage clepage 2856912 Jun  2 09:53 pm1034o.json
-rw-r--r--. 1 clepage clepage   15513 Jun  2 09:52 test1034o.json

The problem is that the binary mask (alpha channel) obtained from
the project file is not re-intersected with the current image being
loaded, so the background remains dirty and appears as black spots
on the repaired image. The same behavior is observed when loading
new1034o.json with binarymask=true.

When loading test1034o.json and recreating the layers from the 
same polygons and new image, a clean alpha channel is created and
the border at the junction of the moved layer is clean. See
clean_background.png. You can reproduce by creating the layer 
for polygon=4 and translating the broken piece.

All the information needed to have a clean background is in the
original json file. Either the layer can be regenerated on the fly
from the polygon based on the new image OR the alpha channel from
the layer stored in the json file can be intersected with the loaded
image using the standard thresholding procedure to detect background.

Last image is cut_voxels.png. Look at the crosshair cursor. There
are complete image voxels and there are incomplete image voxels. 
These incomplete voxels don't make sense to me. How are you obtaining
these subvoxels? The voxels are being displayed in "fast" mode.