My initial thought is that maybe is something wrong with the reboot_to_payload.bin file. Depending if you want to use fusee or Hekate, I would download the latest version of either, rename it to reboot_to_payload.bin, then use that file to replace the one currently in the /atmosphere folderI'm not sure what's the problem but I'm going to ask here either way.
I recently updated my Switch to 12.0.1 (I shouldn't have but oh well) and also everything CFW wise - Atmosphere 0.19.1 & hekate 5.5.5. I did a clean install, formatted my SD card and created emuMMC again. Everything seems to be working well but I noticed, Reboot function from the Switch sometimes won't work? It does reboot the system but every now and then it just stays at blank/black screen after either the Atmosphere logo or Switch logo. I have to turn it off completely and re-send the payload for me to be able to boot. It is very odd.
It only happens when I reboot it using the Switch power menu. If I use Reboot to Payload from hbmenu or from NXThemes Installer it works fine. Not sure what the problem is, I re-did all my installation 3 times already just to make sure and downloaded directly from Atmosphere's and hekate's Github but it still occurs. I even disabled the themes and plugins. I'm actually lost.