Problem: Unsorted bookmarks appear in bookmarks menu, but fail to appear in Library/unsorted bookmarks.
After a virus attack ... and recovery (I'm clean now) I removed (shouldn't have) these files from: bookmarks.bak and files from the .../Application Data\Mozilla\Firefox\Profiles\ca1ytozj.default\bookmarkbackups folder. I then reinstalled 3.6 and imported an html bookmarks file.
The problem started then. Additionally each time firefox restarted, my imported bookmarks would completely disappear and I would have to import them again. So then I uninstalled firefox 3.6 saving personal data & prefs, and installed 4.01.
Same problem with unsorted bookmarks showing in the bookmarks menu but NOT showing in Library/unsorted bookmarks. As to whether my imported bookmarks disappear on a restart of firefox 4.01, I don't yet know because I got started on this problem report.
I think what I need to do in uninstall and choose NOT to save personal data & prefs
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Immediately after posting above I force quit firefox and restarted.
Unsorted bookmarks still appear in bookmarks menu but NOT in Library/unsorted bookmarks.
This time, however my imported bookmarks didn't disappear on the restart. Thanks.
A possible cause is a problem with the file places.sqlite that stores the bookmarks and the history.