System Workbench for STM32

Hello Gshera,

First, update the software, there is a 1.12 version.

Now, about CN12 on nucleo 64, it is 2 GND pins.
I suppose it is a typo error, you meant CN4, right ?

STlink Nucleo CN4 has 6 pins:
Pin 1 is STlink VDD input to measure : To connect to your VDD of custom board
Pin 2 is SWCLK
Pin 3 is GND
Pin 4 is SWDIO
Pin 5 is N_Reset to connect to the Nrst pin of your F405.
Pin 6 is SWO (not needed for debug)

Then, you should have removed the 2 Jumpers on CN2 for STLink usage as you mentionned.

Rgds,
Laurent