STABLE version -- 5.1.1130.129

[Admini]

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?

No, clicking on a bookmark from anywhere will be counted.
There should be something wrong with your cache data.