I have this problem too (glad I'm not the only one, I thought I was
crazy at first). It affects all my applications, from Agave to Zim, even
Firefox and LibreOffice. I just did a unity --reset and I still have it.

I think I have a slight variation from Stephen's problem though:

-If I manually extend the window in a lower workspace to the bottom of
the screen, then move to an upper workspace and call it via the launcher
/alt-tab, I get the problem described above: the window shifts down into
the workspace above it.

-If it's touching the bottom because I used the "snap-to-side" feature,
it does NOT move into the upper workspace - but instead shrinks slightly
so it no longer touches the bottom!

In either case, clicking on the launcher to call the application does
not actually focus on it, and while the application will appear in the
alt-tab screen, it will not me allow to switch to it either, whether it
moved to another workspace or just shrunk.

It's impossible to be productive unless I make extra sure all my windows
are either maximized or not touching the bottom...

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https://bugs.launchpad.net/bugs/834248

Title:
  Oneiric: Non-maximized windows which sit on the bottom edge of the
  lower workspaces shift downwards when called from an upper workspace.

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