Problem with STM32F3 custom circuit
I just stumbled on this thread because I had the same problem and I managed to solve it, at least on my side. I know this answer is probably too late to be useful for you, but for the sake of the future:
those two pins (PA15 and PB4) don't work because their reset state is alternate function (where they work as JTAG pins). So you need to reset their MODER and PUPDR registers (they also have pullups by default). See RM0313 pg. 151.