The dual-monitor problem bothered me from time to time on my office desktop. The maximum screen resolutions are different: one is 1280x1024, and the other is 1600x1200. There is only one dual-monitor option in screen resolution setting, which is 3200x1200, however the monitor with the resolution of 1280x1024 does not support that.
Later, I figured out the reason might be that I selected the one of 1600x1200 as the primary monitor, so that the dual-monitor resolution was based on that. Finally, it worked again after I changed the primary monitor by switching the two cables.
Hacking xorg.conf also helps. I need to add a line in Section "Device" saying:
Option "ParisModes" "1280x1024+1280x1024"