I just confirmed that, if I unmaximize all my windows, and place them
toward the center of their respective viewports, using Super-Numeric
will again properly switch to the correct viewport as well as raise and
focus the selected window.

I routinely change screen resolution from 1680x1050 to 1280x720 and back
again (to clone to a 720p projector).  Also, excepting Terminal, I
generally keep my windows maximized.  Changing resolution like tends to
move all my windows back to viewport 1 (I use, probably like most folks,
a 2 x 2 viewport grid).  I've been using Alt-Space -> Move Windows to
Another Workspace -> Workspace <#> to put the maximized windows back the
various viewports where I like them.  I've noticed, though, that if I
then unmaximize these windows, they often then are just barely on the
same viewport and occasionally even on a different viewport.  I think
this may be the heart of the problem, or at least part of it.

It seems like Unity is determining a window's viewport based on its
unmaximized state and ignoring it's location in a maximized state.  More
generally, it strikes me as a design or implementation flaw to be able
to have a window unmaximized on one viewport and then, if you maximize
it, it ends up on a different viewport.  I can understand how changing
screen resolutions might be an unanticipated way of getting into this
state, but I think that this is something that the Unity Panel should
handle more intelligently.

I also use Compiz' Expo view a lot to reorganize windows, but I don't
think that's the problem.  Others have talked about snapping windows as
being related to the problem.

It seems to me that a picture is emerging here: Unity is not doing a
good job tracking the relation between window geometries and the
viewport(s) upon which those geometries fall.  Expo, snapping windows,
changing screen resolutions: These all seem to lead Unity to get
"confused" re: the mapping from window to viewport and vice versa.


Other bugs I've seen that seem a part of this "cluster" of issues: Bug #799552, 
Bug #802664, and Bug #807442.

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https://bugs.launchpad.net/bugs/791412

Title:
  Does not switch to right desktop upon launcher click, when target
  application is side-window-snapped

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