I dumped the settings for /apps/compiz/general/screen0 with:

gconftool-2 --dump /apps/compiz/general/screen0 > /tmp/screen1

Edited them and replaced screen0 with screen1, then reloaded it:

gconftool-2 --load /tmp/screen1

And it's working! Thank you TJ.
No more screen clipping, however I can't manage Compiz to open the windows
on the secondary monitor. They keep opening on the first one, the only way
to open them there is to force the DISPLAY variables:

DISPLAY=:0.1 gedit

Are you experiencing the same thing, TJ?

2009/4/6 TJ <email address hidden>

> On Mon, 2009-04-06 at 09:56 +0000, Stéphane Travostino wrote:
> > I tried to try the hack TJ explained above, but unfortunately I don't
> > have any "screen1" section in /apps/compiz/general, only "screen0".
> >
> > I am running NVIDIA, no Twinview, displays are :0.0 and :0.1 but I can't
> see this section.
> > I tried to run with two compiz instances with --only-current-screen but
> it's the same..
> >
> > TJ, did you do anything special to have "screen1" show up on gconf-
> > editor?
>
> I don't recall for certain now, but I *think* it was inherited from the
> previously installed release (Hardy).
>
> It is possible to manually create the screen1 keys using gconftool-2, or
> creating the folder and %gconf.xml using a copy of the screen0 settings.
>
> --
> Clipped area for multiple X screens with different dimensions
> https://bugs.launchpad.net/bugs/331918
> You received this bug notification because you are a direct subscriber
> of the bug.
>
> Status in “compiz” source package in Ubuntu: Confirmed
> Status in “nvidia-graphics-drivers-180” source package in Ubuntu: Invalid
> Status in “xorg” source package in Ubuntu: Invalid
>
> Bug description:
> Binary package hint: xorg
>
> On a secondary X screen (:0.1) which has different (larger) dimensions than
> the primary(:0.0), the lower part of the secondary screen is ignored by the
> display manager, remaining black and not displaying windows in that area,
> although the mouse does display in that area.
>
> There appears to be a relationship between the issue and the primary screen
> in that it appears that the height of the primary screen is being used as
> the height of the secondary screen - the black area looks to be 1024-800=224
> pixels.
>
> Not entirely sure if this bug is Xorg or elsewhere. Because it relates to
> running multiple X screens it is testable only with the nvidia driver.
>  However, this is a regression from Hardy/Intrepid in that the same
> configuration on those worked fine.
>
> A picture speaks a thousand words and in this case that is very true.
> Attached are two photographs that demonstrate the issue.
>
> The system has the laptop DFP (1280x800) to the left of an analogue TFT
> (1280x1024). nvidia-settings was used to position the screens relatively so
> the mouse moves between them.
>
> Photograph #1 shows the overview. The secondary screen on the right shows a
> large black band on the lower section of the display where windows cannot
> go. You can see that even the desktop background picture doesn't get
> rendered into that area.
>
> Photograph #2 focuses on the secondary screen. It shows the nvidia-settings
> dialog which is displaying the screen position dialog. If you look closely
> you'll see that the entire bottom section of the dialog window has been
> cropped by the black area, even though the mouse cursor is able to move in
> that area.
>