Hi, really liking yEd so far.
I found some issues though (yEd 3.8):
Create a rectangle
Create a group inside the rectangle (e.g. by dragging a group node from the palette onto the rectangle)
The group is now below the rectangle (i.e. invisible)
Lower the rectangle so the group is visible again
Save, close and reopen the model
The group is below the rectangle again (which is wrong)
Also: lowering and raising does not change the dirty state of the model
And last but not least: it would be nice to have a more convenient way to stack multiple nodes along the z-axis (not just the selected node completely to back/front)