I'm encountering the same problem with Opera 39 as mentioned above:
I customized my speed dial page (new theme, own bookmarks, deleted the standard ones as far as I didn't need them) without any problems, but after closing and restarting Opera the standard page is back again (standard theme and the preset bookmarks). Fortunately my own speed dial bookmarks are still there. Nevertheless, it's pretty annoying to delete the preset bookmarks and change the theme every time I start Opera.
I'm using Windows 8.1 as OS.
Are there any solutions for this problem?