On my latest project I am using STM32F100VCT6 and PB3. I am using this Pin as a quadrature encoder input for Timer 2 combined with PA15. I can not get the encoder to work. I tried setting PB3 up as an interrupt and it does not work, but PA15 does, I then tried setting PB3 as a GPIO and it does not work and PA15 does????? I thought the CPU was faulty so swapped it and still noting from PB3. The input signal is 5V peak to peak, but the datasheet states that pin is 5 Volt tolerant .
I have produced more than 20 designs using various STM32 processors never had this problem before.