This similar to what I am experiencing:
I just upgraded to Lion on my Macbook (White 1.83 2007), I have an external Samsung XL2370HD monitor. The Macbook was sometimes running hot with the lid down with Snow Leopard.
The solution was to lift the lid half way to let it cool, and also to gain access to the built-in keyboard when the external keyboard was not hooked back up. Now with Lion, it switches back to the Macbook LCD display automatically when the lid is opened, and sometimes the colorsync settings get mixed up in the process, causing the second display to be off color until I manually reset the screen resolution to 1920 x 1080.
Also noticed that the ctrl+zoom wheel only zoomed in an area of 1280 x 800 on the samsung set to 1920 x 1080. This seems to be a bug, because restarting with the lid down into 1920 mode, all is well.
I can't find anyway to have the lid open except in mirror mode. Win 7 on Bootcamp works fine and I can lift the lid without it switching. It was very convenient to be able to close the Macbook to sleep it and then click the mouse to wake it on the ext monitor, then sleep and open the lid to wake the built-in display. That is the optimal way it should work, and has worked previously with dual displays.
- Try restarting the Mac in just the external mode (lid closed with pull down menu restart). the lid switch now seems to toggle when you lift and close the lid. So opening it once does nothing, but opening it a second time switches it to the built-in screen, and then a third lift and close puts it to sleep again.
- Click on the mouse in the third sleep mode and it returns to the external display (albeit with resized windows). I believe that Lion may adapt itself (learn?) automatically, which would be very cool, but I suspect that restarting in the different screen modes eventually may help reset the PRAM settings back to normal.
- Also try changing resolutions on both sides. It seems to cache whatever you are doing, and may just be hiccuping on earlier saved PRAM data.
- A last resort is a PRAM reset: Hold alt(option) + apple + p + r on reboot, after the chime. Hold the keys down and let it chime three times before releasing and booting up. BTW, Do this on an externally attached keyboard, lid closed if possible. This will give priority to the external monitor booted, hopefully.