xrandr and xinerama-style multihead are incompatible. My suggestion: get rid of Xinerama.
You're treating both monitors as separate devices, then you're using a kludge called Xinerama to pretend they're on a single GPU. That's neither fast nor bug-free.
Since both screens already run on a single GPU, you can just kill Xinerama and use randr to configure multiple outputs.
Just turn Xinerama off and remove the second device/screen/monitor from xorg.conf, adjust ServerLayout accordingly.
Or is there a good reason why you need zaphod + Xinerama?