STABLE version -- 5.1.1130.129

[QZMTCH]

Accessing from address bar and bookmarks are both counted by default. The reason for not counting accessing from bookmarks may be because you ever deleted the URL from the popular list before (This will reduce the weight of the URL), or the algorithm thinks that you are not interested enough in the URL.

and if the bookmarks are in a folder, and I go to them from a new page that is made by the extension? https://github.com/zombieFox/nightTab like this? the extension stores bookmarks here other bookmarks -> tab 
it turns out that only clicks from the bookmarks bar and bookmarks page are taken into account?