I am also encountering this problem.  It appears that ccsm
(compizconfig-settings-manager) is forcing the window menu setting to
what it thinks is the metacity default.  Changing the metacity
mouse_modifier setting with gconf-editor will work until ccsm is started
again, at which point metacity/compiz acts as if the mouse modifier is
"none".  Using the keyboard to set the compiz Window Menu setting back
to its default will restore default metacity(-like?) functionality.

I ran into this problem when I was trying to set up <Alt>Button2 as
window menu and <Alt>Button3 as window resize.  Metacity doesn't appear
to provide an option for this, even in gconf-editor.  A gconf-editor
search for the text "Button3" only returned compiz keys.  So I think
this problem is potentially twofold: I think there's a deficiency in
metacity because it doesn't allow one to completely disable or reassign
the window click buttons (it only allows changing the modifier), and
second, there's a deficiency in compiz or ccsm that causes the window
modifier setting to go nuts.

The setting in ccsm is shown in blue instead of the normal text color,
which I'm guessing means that the setting is unavailable or problematic.
Another person had a problem with blue settings, referenced on the
Ubuntu forums: http://ubuntuforums.org/showthread.php?t=559273

-- 
Compiz, Button 1 mouse clicks in windows intiates window drag
https://bugs.launchpad.net/bugs/153626
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