When I tried it again 10 minutes ago, after downloading hex file, system simply doesn’t power up. Previously it was only a minor feature that didn’t work. We always disconnect debug tool after downloading firmware, so it is unlikely this was affected by debug tool.
It is tool developed by Elprotroinics. We have been using the very same tool for previous versions with STM32F407 and other STM32 MCUs without any problems. I guess the tool itself can be a source of problem. I will try to verify with ST-link and see what I can find.