I made an icon. In the process grouped some of the elements together, rotated them 135deg, then grouped them again with the rest of the icon layers.
Icon Name [ folder - parent ]
Rotated Layers [ folder - child ]
Additional Layers [ folder - child ]
I then dragged the folder (parent) into another folder of grouped layers. When I did this the "Rotated Layers" (now 3 levels deep) lost its rotation and relative position to one another, scattering them around the canvas.
Grouped Layers [ folder - parent ]
Icon Name [ folder - child 1 ]
Rotated Layers [ folder - child 2]
Additional Layers [ folder - child 2 ]
I found that if I ungrouped the "Rotated Layers", and dragged them into "Grouped Layers" and then re-grouped them, everything worked as expected. So it seems like it is something related to the folders.