My setup: Macbook Pro (current model) running 10.6 with 15" screen at 1680x1050, connected to a 24" external screen (1920x1200) using mini Displayport to DVI. When restating the computer in clamshell mode (lid closed), the resolution on the external screen is incorrect, possibly 1680x150 and shifted to the left, so part of the image is outside of the viewing area and the part that is visible looks bad, because it is not the native resolution. The displays are set so that the external screen is the main one and are not mirrored.
The only way to use the computer is in clamshell mode is to start it with the lid open, log in, then close the lid, the computer goes to sleep, I need to wake it up and the external screen resolution stays correct. This is quite annoying, considering that I was using the same external screen with an old Powerbook rinning 10.4 (miniDVI-to-DVI connection) without any issues.
Any ideas how to fix this?