Comment 8 for bug 331522

please attach your log directly rather than zipping it next time. In your case the xserver has selected a clone mode for your HMDI monitor that matches your VGA port. the digital display may not like the timing. since the monitors are cloned, you'll have to select a different crtc to drive them at different timings. xrandr would ideally be smart enough to do this itself.

if you want the native mode:
xrandr --output HDMI-0 --crtc 1 --mode 1680x1050
or if you want 1280x1024:
xrandr --output HDMI-0 --crtc 1 --mode 1280x1024 --rate 59.9