Comment 2 for bug 1472892

Reproduced with Inkscape 0.91 r13725 on OS X 10.7.5 depending on how the document is opened:
- not reproduced if opened in a new document window
- reproduced if a document window is reused [1]; the correct position is restored if the document is then reloaded via 'File > Revert'

TODO: search existing reports for similar symptoms with 3dboxes - possibly related to the transformation of 'Layer 1' - transform="translate(0,-308.26772)".

<off-topic>
Console message when opening the file:
** (inkscape:32575): WARNING **: Parent of 3D box side is not a 3D box.

Tip: if you want to modify 3dboxes as regular objects (i.e. a group of paths) to e.g. cut one 3dbox face from the group and place it elsewhere on a separate layer, I would recommend to convert the object '3dbox' to path first (menu 'Object > Object to Path'), otherwise the custom 3dbox-related attributes stored with the object (polygon) might interfere with later actions.

Note that - as with any other object (rectangle, ellipse/circle, text, offsets, etc. - 3dboxes converted to path lose the parametric qualities and cannot be edited anymore based on the original object's 3d perspective information, nor can this conversion be reverted.
</off-topic>

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[1] launch inkscape by itself, open document from within inkscape while the initial document window is not dirty (no changes -> document window will get reused to load the file).