Solution (perhaps)
I had the same/similar problem on my iPhone 5 upgrading from iOS 7.x to 8.1.3.
I found that after the upgrade my bookmarks were still in Safari but that my favorites were no longer on the blank start page. After exploring the bookmarks in Safari iOS 8.1.3 I discovered there are now two (2) Favorite folders. The first Favorite folder has a star on the left the second Favorite folder has a folder icon beside it.
The first Favorite folder (with star) is empty. The second Favorite folder has the bookmarks I used to see on my start page in Safari.
My solution was to view the bookmarks in my old Favorite folder, Edit, select the bookmark and change the location to the new (star) Favorite folder. You must repeat this for every folder and bookmark that you want to move from one to the other Favorite folder. Once this is completed the bookmarks, and folders, will be on the Safari start page.
The bookmarks are still on the start page after restarting my phone. Please tell me if this helps with your problems as well.
Regards,
Petar