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Description of problem:
gnome-shell-extension-top-icons.noarch

xchat icon disappears from time to time. Not sure how to trigger it exactly but I hit it every day (after undock and suspend or so). I was told that extensions.gnome.org TopIcon one works well.  

Version-Release number of selected component (if applicable):
gnome-shell-extension-top-icons-3.14.4-13.el7.noarch

How reproducible:
quite often

I've tried to reproduce here, but so far, I've failed. The top icons always reappear after suspend.

This isn't necessarily an extension error, it could be a problem with the sizing of the XEmbed icon itself (see https://bugzilla.gnome.org/show_bug.cgi?id=721596).

Well, we don't know what we're dealing with yet...hard to work around an unknown. Fwiw, I still haven't seen it happen on my rhel 7.2 installation.

*** Bug 1340854 has been marked as a duplicate of this bug. ***

As said in bug 1340854 it happens to pidgin and to spotify as well so that issue seem to be in top icons extension and not the app itself. 
Yeah suspend probably makes the top icon to reappear as g-s restart helps as well.

I also suspected the extension, however, I've noticed the pidgin icon missing also when in standard pop-out tray. So it could be a common issue to these apps.

This is still visible with latest GNOME 3.22 and Pidgin. We need to fix it.

I've found a fix for this for pidgin.

It's a patch for pidgin and it's connected to old notification API pidgin uses.
https://github.com/phocean/TopIcons-plus/files/823156/pidgin_tray_new_style_blink.txt

I will file new bug for pidgin.

Closing, in light of comment 12