Active window "half" looses focus when another one is sent to the front automatically

Steps to reproduce:
 * You need to use some app that gets automatically sent to the front at some moment, like Update Manager or Synaptic. Start updating or installing packages.
 * While Update Manager is downloading, use another app, say Firefox.
 -> At some point, Update Manager gets automatically sent to the front (while updating the cache or starting to install).

Observed behaviour:
 * The unfocused Update Manager window is in front of Firefox (the global menu still shows the menu of Firefox)
 * Clicking on the Firefox window (if visible) or on the Firefox icon in the launcher (if Update Manager or Synaptic is fullscreen) does NOT bring it back to the front.
 * You have to focus the Update Manager window, then click on the Firefox one to put it to the front.

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Desired resolution:

- if an active window is behind another (that is not pinned-to-front) window, any action on it (and a click on its launcher icon) should bring it to the front