I have the same problem after login with the icons disappearing and reappearing following the first mouse move except have an additional delay of 3 or 4 seconds before the icons first appear.
This isn't such a bad problem for me except after creating a backup/clone image to another hard drive with the dd command and trying to run the clone
from another PC, this happens:
I wait the 3 to 4 seconds as usual.
The desktop background appears,
The taskbar appears with the Mate system monitor on it.
The desktop icons never appear.
The Mate system monitor appears and the CPU usage spikes to max, stays maxed, and the Mate desktop freezes up.
I have to <Ctrl-Alt-Backspace> to get out.
(The original PC/Mint Mate image keeps working fine except for the icon flicker on first mouse move after login.)
To trouble shoot the issue with the goal of using Mate as my original user from a clone of my original hdd on a different PC, I do as follows:
From my original PC I Install Xfce,
Re-image my original partition as before and hook the re-imaged hdd to a second PC.
(Everything is done from the reimaged hdd on a second PC from this point.)
I log into the Xfce desktop (with no issues).
From Xfce, I create a second user, reboot, and log into the Mate desktop with no issues.
Then, I add my original user's home directory to /etc/skel and create a third user, reboot.
The original user and the third user login attempts fail in similar fashon.
I hit <Ctrl-Alt-Backspace> to get out.
I log back into Mate or Xfce as the second user and take these steps:
Move a directory from /etc/skel to a temp location.
Create a forth user.
Attempt logon to Mate as that user (user4).
If the login fails,
Replace the previously moved directory back into /etc/skel,
Delete the forth user and the forth user's home directory.
Repeat the process until the Mate desktop fully loads after login.
After deleting /home/user4/.mateconf, user4's Mate desktop successfully loads with no icon flicker.
Even though I have narrowed the issue to my /home/user4/.mateconf/desktop directory on the cloned hard drive, I'm missing important
configurations that I need to keep.
I'm still attempting to find the erroneous config file. Any thoughts or ideas on which one it is?