How does gnome 3 and the window-list extension determine if windows in the window list should be grouped together?

Question

My company recently upgraded from gnome 2 (megacity) window manager to gnome 3 with its included window manager. After the upgrade, we noticed that in the gnome 3 environment with the gnome-shell-extensions installed, (which includes the window-list extension), that when multiple instances of our in house GUI applications are running, they will no longer group together in the window list even after changing the window-list setting to always group windows in the gnome-tweaks tool. What changed from gnome 2 to gnome 3 that would have caused this? How does gnome 3 and/or the window-list extension determine whether multiple open programs/windows belong to the same application type and thus should be grouped together in the window list? Not sure if this is relevant to this question, but I thought I should also note that the icons for our in house applications are no longer appearing on their respective window list button after the upgrade to gnome 3.