Hello - I am sorry for reopening this (it's related to the initial problem). From time to time I am losing (still) the default settings as described above. This seems to happen only and only when I perform the Friday sync.
E.g. Was reading an article, tap to click was working, and the update was running in the background. At some point, tap to click stopped working (I think it was during " [✓] Syncing filesystems" process).
Does anybody else have this issue? @thosol , can you confirm if the same happens to you as well?