Some months ago I only used one monitor with Ubuntu (9.04) and compositing worked perfectly- Compiz and Docky.. everything looked great.

Then I got a new monitor but it wouldn't work with my NVIDIA graphic card so I had to download a new driver. Now dual-monitoring works fine, but the compositing is messed up!

System information: I'm using Linux-x86 with the 180.44 version of the NVIDIA driver and I'm using something called "Xinerama"- and I configure this using "NVIDIA X Server Settings".

I hope someone can help me, I love having two monitors but I also like using subtle compositing- surely it's possible to have both?

What has changed?
From the way you tell it, just the monitor. Then your problem is in xor4g.conf, surely.
If anything else (driver, system) has changed that is suspect also.

The only things that changed were adding the extra monitor and switching between the GNOME Desktop Manager to the NVIDIA X Server Settings

Nvidia drivers are steady enough, and I would read the docs to see if that driver will do what you are trying to do. In particular, if you are loading fewer modules in xorg.conf, I would fix that.

I haven't really used the Gnome Desktop Manager. But it's been my experience rhat when you _really_ need some oddball settings, automated tools fall short.

Look for an example xorg.conf for your setup and copy/convert that to your system specs.