Could it be that the shifted sudoku has multiple solutions? I can align the three layers like a classic sudoku and get the following, which has multiple solutions:
.5. ..9 ..2
... 65. ...
..4 .28 3..
.3. .6. ..7
..6 ... ...
5.. 8.2 ...
... .34 5.9
... ... 12.
8.2 ..1 ...