To replicate: use Midori 64bits for Windows; go to midori://settings -> on startup -> open specific pages and add some web pages. If you close the settings tab and re-open it (or just close and re-open the browser), the open specific pages list is empty.
I have the same problem. I was stocked to see that Midori was completely changed since I tried a few years ago but this not sticking make it mostly useless to my usecase.
To replicate: use Midori 64bits for Windows; go to midori://settings -> on startup -> open specific pages and add some web pages. If you close the settings tab and re-open it (or just close and re-open the browser), the open specific pages list is empty.