I can reproduce this bug though I too had some trouble at first
understanding what this is about. This is using Metacity.
* Add the workspace switcher to your GNOME panel.
* Start gedit and bring it to the front, you'll notice the gedit icon is being
shown in the workplace switcher
* Start alltray and dock gedit
* Show gedit using alltray and make sure it's on top
* The gedit icon will shortly appear in the workplace switcher, but then
disappear
Same for the workspace switcher that is brought up using CTRL + ALT +
Left arrow / Right Arrow, it shows the icon from the program below the
one that is docked (but shown).
** Changed in: alltray (Ubuntu)
Status: Invalid => New
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alltray hides applications from gnome-panel desktop switcher
https://bugs.launchpad.net/bugs/118484
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