I'm running 64 bit Jaunty Ubuntu with Mozilla Thunderbird and Ubuntu's
packages of

enigmail 2:0.95.7-1ubuntu2
 thunderbird  2.0.0.23+build1+nobinonly-0ubuntu0.9.04.1
 thunderbird-gnome-support  2.0.0.23+build1+nobinonly-0ubuntu0.9.04.1

With Compiz "Extra" settings enabled I still see this behavior exhibited
when enigmail pops up to ask for my GPG passphrase (which I have set to
do every time I send an email by choice)

Bug 164489  had been marked as a duplicate of this one, but describes the 
problem specifically with enigmail and thunderbird together.  The temporary 
workaround is to set the appearance/Compiz settings 
System -> Preferences -> Appearance -> Visual Effect = Normal or None

But I wish to enjoy the full desktop effects.

-Joe

-- 
Compiz places transient dialogs behind currently focused window
https://bugs.launchpad.net/bugs/165161
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