Recovering from red light under ON button.
I had this same problem while on a business trip. I was using Android custom ROM and despite the unit was connected to the car charger, the phone was not charging (a common issue in Android... now I know).
Android fully depleted the battery and the phone simply died (no shutdown). When I put my SE wall charger in the plug... horror... a red light pops up under the power button and the phone did not boot-up.
After one hour and a half of trying all of the charger I managed to find, putting and removing batteries and soft resets I managed to start charging again by connecting the phone to my PC.
My explanation of the problem (guessed):
Li-Po batteries needs a minimum power level to work properly and not be damaged, that's why all units have a shutdown procedure when the battery level hits a certain threshold. Android kernel simply don't manage the battery level properly and let the phone suck up all juice from the battery itself until full depletion.
The phone's battery manager is in charge of checking the status of the installed battery even for "dumb charging" through a wall charger and, reading a too low voltage value in the battery, denies both booting AND charging to avoid damages to the phone (maybe it reads the battery as it has a short circuit or the like).
By connecting the phone to the PC, I saw that some drivers were loaded for boot time interfaces (Qualcomm CDMA Technologies MSM). In my understanding, this means that some module inside the phone was powered up using the USB cable even if the "flashing leds" showing charging were not shown. By leaving the phone in this status for some time without turning it on, I managed to bring back the battery to its minimum functional status and I was able to boot it again. The only issue is that the phone will not boot when this status is activated, it needs a battery pull to clear the status.