Behavior was still the same on 6.1.3 except call blocking disappeared, i guess it now checks for phone function. I figured out a workaround for a couple things.

I was able to clear the file scan issue by turning on settings>protection>scan filesystem. However even after turning off the setting again it seems to still scan the filesystem during every scan.

Oddly after doing that the speed test started working as a speed test.

It still prompts me to turn on app locking even though it is on already.

It prompts to start a privacy check even though it has been done and no new apps/updates have been installed since the last time I ran privacy check.