I don't know why they're not sticking for you. They do for me, regardless of Safari Resets, reboots, logging off/on. I do have a suggestion that might make it easier to put them back:This works fine, but when I restart Safari, it clears all the ones that I added manually. How do I get them to ACTUALLY stay?.
- Decide which sites you want and in what order
- Open each of those sites, in order, in a separate tab. (For example, if you choose "Medium" as your Top Sites layout, there are 12 sites, so you should have only 12 tabs open, the first being the first site, 2nd being the 2nd site, and so on.)
- Click Bookmarks > "Add Bookmark For These 12 Tabs" (change the folder name from "Saved Tabs" to "Top Sites"
- Now you have a folder called "Top Sites" with bookmarks for each of your 12 folders, in the order you want them to appear in Top Sites.
- Clear any "push-pinned" site in Top Sites.
- Reset Safari to clear your history and cache.
- Click on your "Top Sites" bookmark folder and select "Open in Tabs"
- Go look at your Top Sites. All the sites should be as you want them.
- If so, Edit Top Sites and make sure they're all "pinned".
From now on, if you lose your Top Sites, just repeat steps 7-9
(At least this is what worked for me! I hope it works this way for others!)
I hope this helps!