Closing lid for clamshell doesn't make external monitor primary under 10.7.3 on MacBook Air 13"
According to Apple Support, the clamshell mode (lid closed) requires:


  
  Power adapter
  External keyboard, mouse, or trackpad
  External display
  


You meet all three criteria. The support article goes on to provide steps for both wired and bluetooth keyboard &amp; mouse combos:


  If you are using a wired keyboard and mouse:
  
  
  Make sure the computer is plugged in to an outlet using the AC power adapter.
  Connect a USB keyboard and mouse to your computer.
  With the computer turned on connect the Apple portable (using the appropriate Apple adapter if necessary) to the appropriate port on the
  external display or projector and turn the display or projector on.
  After your computer's Desktop appears on the external display, close the computer's lid.
  When you close the lid: 
  
  In OS X Lion, the external display will change to a blue screen, then will show your desktop.
  In Mac OS X v10.6.8 and earlier, wake the computer up by clicking the mouse button or by pressing a key on your external keyboard. You
  should now be able to use your Apple portable as you normally would,
  with a USB keyboard and mouse.
  
  


Perhaps you could try opening and closing the lid again.