Hey, sorry to necro this but I've run into a similar issue. More info though:
When I boot into stock, the Sept by Atmosphère splash screen is shown almost immediately (white background) but the white-on-black Atmosphère logo does not. Once the system is booted, the Horizon version string in settings does not include AMS or its version number, indicating that Atmosphère is not launched.
Is Sept actually injected in this case, and will it cause the console to be banned?
(My setup is a bit weird: I followed the
tutorial to manually partition the SD card and install Android and emuMMC side-by-side. However I don't think this should make a difference...?)
Thanks for looking.