Comment 38 for bug 147070

The Compiz devels seem aware of this bug.

I saw this post by Danny Baumann on Compiz's mailing list this evening (post at http://lists.freedesktop.org/archives/compiz/2007-October/002697.html):

(quote)
(...)
Unfortunately I noticed today that release 0.6.0 contains a bad problem
that allows e.g. desktop windows being stacked over normal windows when
they are mapped. This results in normal windows and/or panels not being
visible when compiz is launched with the Gnome or KDE session until the
desktop window is restacked once (e.g. by clicking on it if the "Raise
on click" option is enabled).

I will release a 0.6.2 ASAP that fixes that problem, but until then,
please either apply this commit to the release tarball:
http://gitweb.freedesktop.org/?p=xorg/app/compiz.git;a=commit;h=b6c6acc70261d0942977441914c23e7a1c99215e
or continue to use the compiz-0.6 branch.
(...)
(end of quote)

Hope this helps.