xserver-xorg-video-intel has been updated to 2:2.6.3-0ubuntu9.1 last Wednesday. Since then, XRandR forced the virtual resolution to 2048×2048 and ignored the custom settings in my xorg.conf. This bug hast been fixed on Monday, but is still in jaunty-proposed repository, meaning that you will have to wait a couple of days for it to be pushed through into the main jaunty repo. Alternatively, add the following lines to your /etc/apt/sources.list:
deb http://de.archive.ubuntu.com/ubuntu/ jaunty-proposed restricted main multiverse universe
deb-src http://de.archive.ubuntu.com/ubuntu/ jaunty-proposed restricted main multiverse universe
Remember, this only resolves the problem with XRandR in a simple dual-head setting. If you also want to run Compiz at this resolution, you may want to use my custom packages. I have updated them to work* with the current Jaunty update without setting them on hold.
* Please beware – these drivers may crash your X11. I have only tested them with recent Lenovo Thinkpads (T400 and X200), and there have been no issues. But this patch has been reportedly crashing other systems.