Comment 15 for bug 556253

@Martin:

This sounds like it could be partly gnome-settings-daemon misbehaving. g-s-d performs the xrandr configuration for the gnome desktop. I've been working on bug 484186 where g-s-d will fail to change the configuration settings of a CRTC output. You may be seeing the same bug from the DVI side. I've built a test package with my fix and uploaded it to ppa:chasedouglas/gnome-settings-daemon. Would you mind trying it out to see if it helps?