The switch is not booting normally because of AutoRCM. You are no longer seeing the SX OS menu because it automatically boots the Switch into CFW when your license is activated. In order to allow the Switch to boot normally, you must remove AutoRCM. To do that, you need to boot into the SX OS menu. Simply hold volume + while sending the SX Loader payload and it will pop up. Then uninstall AutoRCM. Now your Switch will be able to boot back nornmally.
While there is no fix, if they have a GitHub page, it might be worth reporting the error there to let the developer know there is a problem with their software in the hopes they can fix it in a future update.
Factory resets do not actually fully clear the console, contrary to popular belief. There is currently no known method for completely wiping the Switch of all traces of hacks. So far, I would say the best option is keeping a NAND dump prior to performing any sort of homebrew or hacks but if you have not done so already and used any sort of homebrew/hacks, then it is too late and you will have to wait to see if the community can come up with something.