Comment 3 for bug 250863

I had this exact problem. I found that changes to the bookmarks did not hold over to the next session. Weirdly enough, they would hold over if I did a bookmark backup, though (without having to import that backup).

In any case, I got tired of backing up my bookmarks any time I wanted to change them, and I couldn't find a solution posted, so here's my solution, which seems to have worked:

1) Save your bookmarks and anything you wouldn't want to lose then close firefox
2) Delete the directory .mozilla/firefox from your home directory
3) Restart firefox

This will delete all of your settings and bookmarks, but for me at least it also fixed the problem.