I have the same thing and I'm running kubuntu 14.10 (although I also had it 
when I was running 14.04.) 
When I try to do the initctl mentioned above I get this:

root# initctl restart indicator-application
initctl: Unknown job: indicator-application

I also noticed that it appears that a lot of my session is pre-loaded
before I login. If I login to the command line I have a lot of processes
running, even though I have not logged into the GUI.

** Changed in: unity
       Status: Expired => In Progress

** Also affects: meta-kde (Ubuntu)
   Importance: Undecided
       Status: New

** Changed in: unity (Ubuntu)
       Status: Expired => In Progress

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https://bugs.launchpad.net/bugs/1357681

Title:
  System tray icons for Owncloud, Insync and Dropbox disapear after
  reboot

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