I can confirm the same problem. Looks somewhat similar to Bug #127445
(https://bugs.launchpad.net/ubuntu/+source/compiz-fusion-plugins-
extra/+bug/127445) but that was fixed a while ago. I am using Jaunty and
unchecking the Show desktop option within Scale will "fix" this - by
which I mean the windows no longer go awol. However, the potentially
useful behaviour of directly accessing the desktop by clicking on it is
of course no longer possible.
** Changed in: compiz-fusion-plugins-extra (Ubuntu)
Status: Invalid => New
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Compiz Scale: Windows not reachable after scaled view
https://bugs.launchpad.net/bugs/195122
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