I tried unplugging my secondary display, and the icons appear. They are also arranged much more in a grid, whereas with both monitors plugged in, the icons were displayed somewhat randomly.
When rebooting with my secondary display disconnected the icons appear.
Re-connecting the secondary display (without rebooting) messes up the order of the icons again.
This issue seems to be related to dual-monitors.
I tried unplugging my secondary display, and the icons appear. They are also arranged much more in a grid, whereas with both monitors plugged in, the icons were displayed somewhat randomly.
When rebooting with my secondary display disconnected the icons appear.
Re-connecting the secondary display (without rebooting) messes up the order of the icons again.