After updating to JB, I too was having proximity sensor issues.  After a few weeks I finally got fed up with it and did a factory reset of my phone, but the proximity sensor issue remained.  I also have had a Zagg HD screen protector on the phone since day 1.  It is the old style with the small cutout for the sensor.  I removed the Zagg HD and got a new Zagg (non-HD).  The new protector I bought still had the old cutout, but I made the cutout bigger to so that it did not cover any of the proximity sensor.  After installing the new shield with a bigger cutout, my proximity sensor issues have disappeared.
This is only my experience and it worked for me. If you have a screen protector on your phone and you are frustrated by the proximity sensor issues, it may be worth giving a shot.
				
			This is only my experience and it worked for me. If you have a screen protector on your phone and you are frustrated by the proximity sensor issues, it may be worth giving a shot.
	