The first time it runs it should not sort bookmarks until the user would indicate it Rated 5 out of 5 stars
The extension works as it should. But the fact that the first time it runs it sorts all your bookmarks -included those of the Bookmarks toolbar- makes it somewhat dangerous if you want to keep the manual order of some bookmarks. Later you can disable the sorting of the Bookmarks toolbar's bookmarks, but it forces you to restore your bookmarks, either with the automatic backup done every day by Firefox, or by a manual import.
UPDATE: on last versions the autosort function need to be activated, solving the problem of unwanted sorting of the Bookmarks toolbar. You get now 5 starts!
In version 2.0.2, the extension ask the user a confirmation before activating the auto sorting option.