To rule out a database problem, could you let us know what you get when you run the "Verify Integrity" function. That's here:

Open Firefox's Troubleshooting Information page using any of these methods:

• "3-bar" menu button > "?" Help > More Troubleshooting Information
• (menu bar) Help > More Troubleshooting Information
• type or paste about:support in the address bar and press Enter/Return

Near the bottom, there is a section titled Places Database -- that's the file which stores history and bookmarks. Click the button labeled Verify Integrity. There may be a 10-15 second delay before results appear.

If all is well, the report that appears below the button should start with:

> Task: checkIntegrity
+ The places.sqlite database is sane
+ The favicons.sqlite database is sane

Does yours say that, or something else? You can select and copy the report, and then paste it into a reply for review and comment.

Ok, that was helpful, thanks. What I found out is that my moz_bookmarks table has 200 entries which I found to be strange, since I could not get to import any bookmarks at all. So I closed Firefox and opened my places.sqlite file with sqlitebrowser and saw that it has all my bookmarks there in the moz_bookmarks table. On Linux this file is located in ~/.mozilla/firefox/YOUR_PROFILE/places.sqlite So i opened Firefox again and opened the bookmark manager (Ctrl + Shift + O) and there under "Bookmarks Menu" was a folder with all of my imported bookmarks. Then just select them all, cut and paste into "Bookmarks Toolbar".

TLDR After importing your bookmarks from HTML check the "Bookmarks Menu" section. A folder with all your imported bookmarks might be there.