I have to ask again, what red notification light? My N4 has no such light while charging.
If my phone is in a "powered on" state (sleeping perhaps, but not powered off), the screen will wake up when I plug in and a small white lightning bolt appears across the green battery icon.
If it is powered off (totally dead or press and hold power button while on until pop up menu appears and then select "Power Off"), when I plug in I see a large animated battery icon drawn in white in the center of an otherwise black screen. The icon disappears after a minute or so and then reappears briefly every few minutes.
If you guys are waiting for a red notification light, I can only assume that you have Lightflow or a similar app installed. This is just an educated guess, but I would assume that Lightflow, being a software app and not a part of the phone's firmware, is non-functional when the phone is in a power off/dead battery mode.
Now, just for the heck of it...
Last week I installed this iBlason case
Amazon.com: i-Blason Slim Fit S Line Flexible TPU Case for Google Nexus 4 Smart Phone E960 LG 8gb 16gb (Black): Cell Phones & Accessories (although it was only $9.95 when I bought it, now it is $12.95??). It has a nice sized cutout at the bottom for the micro USB connector; nevertheless, I have found that some of my USB cables have more bulk around the connector than others and so some of them either barely make electrical contact when plugged in to the phone - as in the slightest movement will break the contact and stop the charging - and one of my cables simply cannot make electrical contact unless I remove the case.
Any chance any of you guys are actually dealing with a similar issue?