I had this same problem on my 6.2 MBP. It has an nVidia card. If your using an ATI model then I am not sure.
First reset your NVRAM and SMC just to make sure your not having issues left from installing or setting from OS X, or anything like that. Keep in mind that neither of those should be done too often, but once in a while doesn't hurt, and because linux doesn't "store" any of it's configuration there it should be fine. Remember OS X will have some settings reset.
Next make sure you install nvidia-experimental-304 or better. Earlier versions did not detect monitor hot plugs over the display port (for me).
Remember that all the "Mac" rules still apply. You can not close your lid on battery and have the laptop stay on, no matter what you do.
Now for configuration. Go to System Setting then power management and make sure to disable suspend when lid is closed and on power. Might as well leave it active on battery as nothing is going to stop that.
Now make sure you have a keyboard attached and close your lid. Your laptop screen will go black as will your external monitor. Press a button and your monitor will go on (this is a hardware feature OS X does this as well).