Comment 13 for bug 1754458

The offered solution of changing the panel style did not persist after restart. The following has solved the problem for me, with the solution persisting across sessions/restarts.

I discovered I had two version of the file: "indicator-application.desktop", apparently one from an earlier install. I removed the old version:

sudo rm /usr/share/indicator-application/upstart/xdg/autostart/indicator-application.desktop

I'm not sure if this actually contributed to the solution, the main fix was to start up the indicator applet with dbus-launch. I edited the other file:

sudo pluma /usr/share/mate/autostart/indicator-application.desktop

I changed the following line:

Exec=/usr/lib/x86_64-linux-gnu/indicator-application/indicator-application-service

To instead say this:

Exec=dbus-launch /usr/lib/x86_64-linux-gnu/indicator-application/indicator-application-service

That fixed the missing nm-applet icon in the tray. I had a program that automatically starts that puts an icon in the tray. Its icon was still not appearing in the tray, so I set it so that it is delayed at startup for 10 seconds until the tray and indicator applet is loaded. This seemed to fix the problem. To do this, from the Control Center, select "Startup Applications" (or directly edit the file in ~/.config/autostart). Edit the command that Ubuntu Mate uses to execute the program using the following code (and you can change 10 to whatever delay in seconds you'd like):

sh -c "sleep 10 && NAME_OF_PROGRAM"