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This question and my very tentative (dubious even to me) speculation that the cause might be the main polyfuse on the 5V regulated supply common to all (?) Raspberry Pi's left me wondering about how power to the USB ports is regulated. I'm aware that using:

max_usb_current=1

Supposedly allows up to 1200 mA to be drawn in total through the four USB jacks for the newer models (+/2, and I believe by default on the higher amped 3). I know this will support, e.g., a USB spinning disk drive (~300-500 mA), a wifi adapter (~100-200 mA), a keyboard, and a mouse (~50-100 mA each) simultaneously without trouble with a 2+ A supply.

I believe the +/2 models are rated at 2A, and the intention of the polyfuse is to prevent sudden or sustained current draw beyond that. Presuming the SoC itself is capable of reving up to 7-800 mA, and the 3.3V rail is also regulated to < 150 mA, that should mean the only chance to really draw too much current is via the 5V rail.

Would it be possible, in the context of the linked question, where enough devices to exceed 1200 mA are connected up via USB, to exceed that limit? I notice max_usb_current=1 is not "officially" documented, and that while not using that setting (i.e. =0) clearly does limit the USB output (it is hard to get an external HD to work without it), using it may essentially mean total USB current isn't regulated beyond 500 mA per port, and the "1200 mA" from around the web is a recommendation because, of course, the whole board should be operated at < 2 A (or 2.5 A for the 3).

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max_usb_current=1 has no effect on the Pi3, as the USB Current is regulated by a different chip AP2553.

It was possible to fiddle the current on the Pi2 because the current was set by switching in an extra resistor when max_usb_current=1 is set. See https://raspberrypi.stackexchange.com/a/46752/8697 for some further comments. (Actually the current on the Pi3 is also set by a resistor, which potentially would let you fiddle it, but as the total current draw is limited by the polyfuse seems rather pointless.)

The Pi2 has a 2A polyfuse, the Pi3 2.5A. Unfortunately the published schematics are incomplete, and not all the wiring is shown, but physical inspection of the board confirms these speculations.

These control chips have two modes of operation; either limit current (and thus drop voltage) or shut off supply on overload. There is no (easy) way of determining which is used.

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