I have been living with this issue for some time now, finally annoyed me
enough to Google and found this bug (thanks for reporting :)). Alt-f2 r
also fixes for me which is a new workaround that I'm very grateful for.
In my case it seems to be related to extensions which manipulate the top
bar (e.g. todo.txt / system monitor). If I disable all extensions, and
reboot the box, its fine. If I enable one of the extensions after
rebooting and logging, it looks fine but after reboot, no application
icons will be there. Previously I had just assumed they were broken
extensions but seems to happen with quite a few of them and i have seen
with many different combinations of extensions.

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https://bugs.launchpad.net/bugs/1801757

Title:
  all app indicators disappear

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