Hi this is a bug of the older noggit version.
Try to contact Steff here in this forum to apply as a beta tester.
Or you can Fix it by Just saving the saved adt again. Everytime you save the "shadow" gets inverted,so if some parts are missing ,just set brush speed in raise/lower to 0 and the brush size to very big.
Shift+click to remove the shadow and save it. Reenter the location(you should see the shadow in noggit too) and save the affected adts again.