I experience exactly the same problem. I have been messing around with
Arch Linux for the past few weeks (w/ GNOME 3.24), and despite my best
efforts I haven't been able to solve this bug/glitch. Repeated (latest)
installs, but no luck. Have you made any progress?

One thing that may be related is a strange Nautilus error message when
one attempts to rename one of the desktop icons for the first time. Try
the wastebasket, for example, and let me know what happens for you.
Regards.

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You received this bug notification because you are a member of Desktop
Packages, which is subscribed to nautilus in Ubuntu.
https://bugs.launchpad.net/bugs/1696621

Title:
  Desktop icons slip under the top bar after logging in

Status in GNOME Shell:
  Confirmed
Status in gnome-shell package in Ubuntu:
  Confirmed
Status in nautilus package in Ubuntu:
  Confirmed

Bug description:
  Desktop icons slip under the top bar after logging in again.

  If I place icons on the desktop in Gnome Shell they look fine, until I
  log out and log in again. On the second login they have moved half
  under the top bar.

  The same problem is visible in the Ubuntu live session starting with
  20170607.

To manage notifications about this bug go to:
https://bugs.launchpad.net/gnome-shell/+bug/1696621/+subscriptions

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