To repeat bug:
(Attempting to create a perspective drawing using 3D Boxes.)
Start Inkscape. New project.
Doc properties: Display units inches. US Letter. Landscape.
(Creating guidelines to vanishing points.)
Create closed path: 5.5,6.0 to 5.5,4.0 to 0.5,5.0 to 5.5,6.0
Create closed path: 5.5,6.0 to 5.5,4.0 to 10.5,5.0 to 5.5,6.0
(Placing 3D boxes using the vanishing point guidelines.)
Create 3D Box, place and adjust so that apex is at 5.5,6.0. Set left vanishing points to 0.5,5.0 and right vanishing point to 10.5,5.0. Left panel (width) to 4.4 and right panel to 6.6.
(Copy the box and place others within the paths defined by the vanishing point guidelines.)
Select 3D Box and copy to clipboard.
Paste clipboard. Position pasted box within guidelines. Adjust size appropriately such that it just touches the adjacent box(es)and the guidelines. Seven boxes total.
(Save work.)
File, Save As (whatever).
Close Inkscape.
Shutdown PC.
Startup PC. Login. Invoke Inkscape.
File, Open Recent (whatever).
BUG: The 3D boxes are not place within the guidelines, they are positioned by Inkscape below the guidelines. (In my original project that I observed the bug in, the guidelines were at the bottom of the document and the boxes were placed off the document page!)
Note that if the .svg file is opened with say Internet Browser the 3D boxes are correctly positioned. It is the reload (reopening) of the project by Inkscape that fails to properly position the boxes.
(attaching file.)
Reproduced in Inkscape 0.92.1 r15371, Win 8.1, 64 bit.
Opening file from shell looks ok.
Opening file from within Inkscape shows objects misplaced, provided test file is not currently open.
When the test file is open in one instance of Inkscape, opening the test file in another instance looks ok.
TD