Comment 1 for bug 110088

The current X configuration system runs only at install time, so if you swap hardware after installation, problems like this can occur.

You did the right thing to run X -configure or dpkg-reconfigure. However, sometimes your monitor doesn't get detected (see bug 3731), which results in the suboptimal resolution and refresh rates. As a workaround, if you edit your /etc/X11/xorg.conf file you can fix the refresh rates for your monitor.

Longer term our hope is to make use of Xorg's built-in hardware detection, making all this reconfiguration work unnecessary. See bug 3731 for details.