Try to switch Kodi resolution (the GUI) to 1080 30hz instead of 1080 60hz in kodi settings.
At least it worked for me, even though I can't find a direct relation to kodi GUI resolution and Hyperion...
Thanks for the suggestion, changing refresh rate to 30Hz fixed the problem of screen flickering!
TPmodding, I'll explore the github to see if I can fix Leds flashing on SPI mode.