Almost year passed and I solved the issue today. Unfortunately I had to drop Espruino and stick to low level HAL STM32 library. The LED pin is controlled by timer's PWM and DMA. If you invert the timer polarity simply changing one register everything starts working. I want to say a HUGE thanks to everyone who helped me with this problem. You guys are awesome. OMG I can finally finish my clock now, I am so happy!
I will post the clock here as soon as I finish them.
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