Ok, I've tracked this down to Unity and found the root cause.

Both the panel and the launcher window struts are wrongly initialized
with the BaseWindow default geomentry (100,100,320,200) causing sporadic
compression of desktop icons in the lower part of the screen. This is
due to that the panel/launcher geometries for their BaseWindows have not
been set when corresponding struts are enabled. Those geometries are
availble in the code sequences so this patch just rearrange the order to
see to that the geometry is set before struts is enabled.

Attaching the patch "icon_container_size.patch".

** Patch added: "icon_container_size.patch"
   
https://bugs.launchpad.net/ubuntu/+source/compiz/+bug/886667/+attachment/3076721/+files/icon_container_size.patch

** Also affects: unity (Ubuntu)
   Importance: Undecided
       Status: New

** No longer affects: unity (Ubuntu)

** Also affects: unity (Ubuntu)
   Importance: Undecided
       Status: New

** Changed in: unity (Ubuntu)
       Status: New => Confirmed

** Changed in: nux (Ubuntu)
       Status: Confirmed => Invalid

** Changed in: compiz (Ubuntu)
       Status: Confirmed => Invalid

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https://bugs.launchpad.net/bugs/886667

Title:
  boot moves desktop icons

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