I got a workout. The problem was only when I saved bookmarks with ctrl+D. It saved them in different place. When I clicked the "+" near bookmarks toolbar it worked as if I used ctrl+D before 25 update.
I'd like to go back to Opera 24. Or at least change how bookmarks work now. I preferred the preupdate way and I just hate how it works now. I can only edit my old bookmarks and any new are saved in a different place.