I have nVidia's Twinview configured and running for two different monitors. This allows for two distinct desktops while still allowing for seamless sharing. With 2.6.3, I can maximize an app and it will resize correctly to fit the one screen. Later versions, the app will span both monitors.
Steps to Reproduce:
1. Configure Twinview
2. Upgrade to Gnome 2.6
3. Maximize an app and observe the spanning accross both desktops
Should maximize on the correct monitor
your 'emerge info' ? Always provide this, read the bugreport form carefully.
Try re-emerging metacity with xinerama in USE.
Still happens if Xinerama is enabled.