So step thru the manual process again and describe what you see at each phase please.
Do the STDFU phase, and write the new loader. Then re-power the device and show us the device in Device Manager.
Open FezConfig and “Check device for update” and show us the result of that; then deploy the firmware.
I have stepped through this with an STM32F427 device on Windows 8.1 in the past week, without issues. It seems to me to be either your PC USB ports or drivers, or possibly even the USB cable you’re using. Are you sure you’re using a high quality, heavy duty, USB cable (I have some light weight, dodgy eBay purchased cables that are woefully unreliable, they aren’t worth cutting up for scrap !).