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).
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).