I have noticed the same thing. It can be one of several things, but I have not been able to pinpoint which one.
1. I know that the (I think) ambient light sensor is ripping off of the cable when I am removing it from the old phone. This could be causing a short.
2. The other thing that could be causing this (more likely) is a little white rectangular piece of paper/plastic (?) that needs to be transferred from the old front to the new one. I think this does something like filter the light through the right way. I have noticed it makes a difference, but doesn't always fully fix it.
3. Finally, sometimes scratching off the paint on the pinhole of the screen allows more light to come through, but this is also hit or miss.
Sometimes putting the phone back together with a shattered front on it allows it to work again. This leads me to believe that the fronts are defective. I'm interested in hearing more from other techs working on these as well... really weird issues. Proximity has always been a problem on the GSM 4, (sometimes CDMA, very rarely 4S). I saw it pop up again on the 5/5s/5c fairly often...