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I've been having some weird troubles with indicator icons. I'm using 12.10, but this has been happening since 11.04 came out.

Two applications, Skype and JungleDisk, have little icons that sit in the system tray in the top right corner of the screen. I have added them to the system-tray whitelist in dconf-editor, so they do show up, at least initially.

The problem is that both icons disappear sometimes. This happens even when the applications are open with a visible window - the icon just disappears from the tray. The apps still work, they send notifications, etc, but the icons are gone. It's especially annoying with JungleDisk, because once the icon disappears, the only way to interact with the program is to kill it manually, then relaunch, and open the window before the icon disappears.

Here's the strange thing: if I open the Dash, or hit Super-S to expose all of the workspaces, you can see the icons again. Screenshot with Super-S: icons visible in tray after Super-S

and screenshot while Dash is open: icons visible while Dash is open

While the dash is open, the icons in question seem to be sort of hidden by the panel.

Anybody run into this before, or have any thoughts on how to fix?

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Does this happen only with some certain applications, like Skype? Or does it happen with all possible indicators? – DoDoGo Oct 29 '12 at 20:36
Only with Skype and JungleDisk. – MTS Oct 29 '12 at 20:37
AFAIK this is because neither is an indicator and they have a been implemented in a hacky way, via sni-qt. Maybe try purging sni-qt and installing it again, see if that helps. Don't forget to log-out/in afterwards (or restart unity). I'm not putting this down as an answer though, since it's just a random suggestion. – DoDoGo Oct 29 '12 at 20:46
Seems to be working so far. Thanks for the suggestion! – MTS Oct 29 '12 at 21:45
OK, after a whole day, the icons disappeared again. Sigh. – MTS Oct 30 '12 at 19:50

You appear to have hit this bug: Unity Bug #932769: tray area disappears after alt+tab in fullscreen window.

Unfortunately, nobody seems to know a solution so far.

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