Found what is going on: Desktop-Directory and Desktop configuration files are 
read concurently. Since desktop icon positions are not read at first, read 
files in Desktop-Directory are sorted default (top-left -> down-left). At some 
point at least one icon position is found (reading is concurent!) and then 
resorted. This leads to an event writing out the "new" positions of the icons, 
overwriting everything with new values. Since some icon positions where read 
before the icons where placed, these remain intact. Other icons where read 
before the icon positions where known these are sorted by default.
Result: some icons keep there places, while others are sorted by default.
At least one icon may be recognized as "moved" the icon position file is 
overwritten with the icon positions known by now.

This is a race condition: reading config-files races against reading
desktop directory. Normally, with no load reading config files wins. But
if some background processes are started this isn't true any more --
directory reading is faster, than configuration file reading with the
result of resorted desktop icons.

The system shall make sure not to place any icon until it has read all
configuration files holding icon positions. After these are know it can
continue placing icons.

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https://bugs.launchpad.net/bugs/1335492

Title:
  xfce4 looses desktop icon positions from time to time

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