arranging bookmark folders

I'm running Mountain Lion and Safari 6. I keep my regularly used bookmarks on the toolbar, and all the rest in a folder (called ATR) also on the bar. Within the folder are sub folders arranged alphabetically by name. I've been using this system for years. Recently I added two new sub folders to ATR, Photography and Military. They appear at the top of the list rather in the correct order. I go into Show all Bookmarks, drag them into the proper place and they immediately pop back to top of the list. Never had this problem in Safari 5. Can't make the folders stay in place. What gives?