I have the arc theme installed and the numix circle icon pack. Sometimes, when I boot up the system, the desktop looks like this (note also how bad the text looks):

desktop at startup

However, if I do from the terminal sudo service lightdm restart, everything is normal as expected:

after restarting lightdm

This didn't happen some days ago, maybe it's something I installed. This also happened sporadically on 14.04, but now is more frequent.

How can I solve this, or at least how can I try to figure out what's wrong?

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Same problem here. Icons back to stock and cannot be changed at all. Weird – RobAu Jul 19 '16 at 6:43
    
sudo service lightdm restart fixed mine. I also experience this frequently – Kasun Siyambalapitiya Jun 17 '17 at 10:14

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