Comment 6 for bug 394490

Same here on MSI PR201 with Intel graphics and GM45 on Xubuntu 9.04:

xrandr --verbose --output VGA --auto --output LVDS --off

crtc 0: 1440x900 59.9 +0+0 "VGA"
xrandr: Configure crtc 0 invalid time
crtc 0: disable
crtc 1: disable
screen 0: revert
crtc 0: revert
crtc 1: revert

I have to add that few simple calls work:
xrandr --verbose --output LVDS --off
crtc 1: disable

xrandr --verbose --output VGA --off
crtc 0: disable

And for those who need to change few things surprisingly granrd (xrandr gui frontend) still can change res and reactivate deactivated outputs. In my opinion this bug is due to some new stuff in edge xorg or edge intel driver, as downgrading to:

xserver-xorg-core 2:1.6.0-0ubuntu14
xserver-xorg-video-intel 2:2.6.3-ubuntu9.3

solved this trouble.

Hope this helps