Comment 12 for bug 166691

I think I can confirm bug in Inkscape 0.48+devel r on Linux Mint 13 Maya (Gnome Shell)

The way I found I can reproduce the bug is by manually dragging a layer to the bottom to reorder its z-index. The layer list does get reordered but in reality the layer in question keeps its original z-index. Clicking on the arrow to "lower the current layer to the bottom" fixes it.