Just to give my experience, I have the red light on mine, but I never noticed it before the update so I can't say for sure whether or not it was a result from 4.1. I believe I would have, though, as it was extremely obvious to me last night just after the update and using the phone in the dark.
As for my proximity sensor, it seems slightly worse off than before. It failed within the first minute of a call (quicker than it ever had before), and at moments would flash on and off every 2 seconds (also quicker than it did before and for longer).
Note: I perform all of the major updates like this by putting my phone into recovery mode, restoring my phone, and setting it up as a new phone as opposed to restoring from a backup to ensure a clean installation.
(Probably just going to take my phone in to be replaced because this issue is becoming ridiculous)