This problem appeared after update of Xubuntu to 14.04.
Some applications work correctly(for example, PSI+ or Skype, which are both Qt). But such applications as shutter and tomboy don't have their tray icons, but they are running.
See also: Bug 11298
Created attachment 7040
Panel showing missing icon images
This is as normal when booted up.
Created attachment 7041
After properties resave
This shows the icon images appearing after going into properties and re-finding the icons and re-saving the settings, and what it should be like all the time.
My post was not saved, so here goes again.
I was going to create a new bug, but this one does explain the problem pretty well. The fact is that it has to do with all panels, not just parts of one.
Please see attached screenshots.
I forgot to mention that I am using Xubuntu 14.04.5 64-bit.
This seem to be two different reports (one is about a launcher, the other about some apps not providing trayicons or not displaying them..?). Either way, I see little chance at fixing this.