I get the same issue on a Pi 2 Model B.
There is no more +5V power on the USB socket. I read the other posts which speak about AP2553 :
The signal on pin EN is a rising edge which decreases after +/- 10 ms. The cycle is about 250 ms.
Nothing connected on USB port. See picture below :
I though something was consuming current. So, I have placed a simple 150R resistor between +5V (PIN 2 GPIO) and PP27 (VUSB)
I measured the voltage drop which is about 1 V. 1V/150R gives less than 10 mA. I do this test without SDcard (so not running and can explain this low current as there are less power consumed by IC ).
But, it shows that there is no over current and VUSB appear from AP2553 by cycling and gives only 4V.
This is the resistor placement :
Finally, I place a resistor of 1R between +5V and VUSB. When there is nothing connected, VUSB is +/- 5V.
When I connect a Wifi Dongle the power fall at 4.91V.
When I start the Rpi (SDcard inserted), VUSB fall up to 4.7 V for a short time (I suppose other IC are powered ON).
The Wifi dongle is detected corretly on 3 USB port but not on the upper USB socket near the RJ45 connector. I don't have an explanation.
Question : I don't understand which component is wrong : AP2553, the Rlimit, a capacitor, the sense current,...