Made some more tries:

1) Reinstalled to see if the former tryout to enable desktop effects could have 
troubled something, fresh reinstallation, just installed xorg-driver-fglrx, 
rebooted and the beahviour was the same... thus... could it be a matter of 
interaction between fglrx drivers and the launcher? Could I try tweak something 
in the relevant section in xorg.conf (that it's correctly almast empty, these 
days)?
2) Tried to enable/disable the maximus options in gconf to no_maximize and to 
un-decorize, the only way I can get a usable desktop is by never maximize and 
never undecorize the windows... 

Sometimes, if the app is already open, and I hit the maximize button,
the windows maximizes as it should... but, if I (even with maximus
instructed not to maximize windows) open a program that starts already
maximized (because I closed it from a maximized state) the problem still
occours... this leads me to guess that's not a maximus issue, but
generally an interaction issue between metacity's maximized windows and
what appens to netbook-launcher when an app starts maximized (or gets
maximized by hand, because, as told, sometimes, even when I maximize it
by hand, the bug shows up!)

Another, related IMHO, issue is that, whenever I run an app that needs
sudo password (like synaptic), I have to be really fast in writing the
password, since the box would disappear in few seconds, but it's still
interactive, actually, since if I hit return, it performs the right
action (if I entered the right password, without watching the dialog, it
opens the app, if I hitted the wrong one, it tells me to retry..), in
this case, however, the only difference with disappearing windows is
that the netbook-launcher is never faded, but remains full color
(probably becuase the dialog is not considered a window...)

-- 
Maximized windows disappear
https://bugs.launchpad.net/bugs/364921
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