I upgraded system from 17.04 to 17.10. Sometimes after login to Gnome3 I dont see tray icons. And it looks like this:
Only standard Gnome applets are visible. After logout and login again it back to normal, like this:
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Problem was in old Unity
indicator-application. Because I used Unity earlier in 17.04 and upgraded to 17.10 this indicator wasn't removed. I still have Unity available. After disabling
indicator-application from autostart now legacy tray icons works fine. To disable autostart of this indicator remove
/etc/xdg/autostart/indicator-application.desktop file from system. Now it works with standard
Ubuntu Appindicators Gnome extension.
The issue is caused by an old Unity app-indicator which is in the system autostart. Remove it with
sudo apt remove indicator-application and reboot.
Only removing the config setting
/etc/xdg/autostart/indicator-application.desktop as suggested in the another answer is not very clean and may cause issues later on.