Hi Petr,
I am using pins of J3 port and the pins are,
2 - PA12 - Interrupt
5 - PF3 - Chip Select
7 - PF0 - MOSI
9 - PF1 - MISO
11 - PF2 - Clock Out
13 - GND - GND
When compared the schematics for both revisions, there are no differences for the SPI connections i.e. for J3 connections. Only differences are for usage of latest MCU silicon, additional features of SD card etc for revision D board.
I am trying to read device ID/signature of a flash memory connected over SPI interface. I have implemented a loop of 5 for reading this value. With rev B board, it works fine for all the 5 times but with rev D board, it works for the first time after power up.