Yes it does, I owned several android phones I've rooted all of them and this is the first time it happens. The idea is once you give root permission to settings everything works ok. Just don't open settings immediately after phone boots up. Just give it a minute or two to open settings or after you see the toast showing settings have been authorized root access.
ive noticed my apps lose their permissions in SuperSU... i have tibackup set to run once a week on sundays, and once a month it says it failed to acquire root privileges, though i dont mess with it.
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