If you use Sync then best is to disconnect Sync temporarily during troubleshooting.

You can check for problems with the places.sqlite database (bookmarks and history) in the Firefox profile folder.

• use "Verify Integrity" on the "Help -> Troubleshooting Information" (about:support) page
  in case errors are reported close and restart Firefox and retry

See also:

• http://kb.mozillazine.org/Locked_or_damaged_places.sqlite
• https://support.mozilla.org/en-US/kb/Bookmarks+not+saved#w_fix-the-bookmarks-file

If "Verify Integrity" on the "Help -> Troubleshooting Information" (about:support) page cannot repair places.sqlite then remove all places.sqlite files in the Firefox profile folder. Firefox will rebuild places.sqlite and restore the bookmarks from a recent JSON backup in the bookmarkbackups folder.

• keep a backup copy of places.sqlite in case a new places.sqlite database has to be created
• http://kb.mozillazine.org/Unable_to_process_the_backup_file_-_Firefox

You can use the button on the "Help -> Troubleshooting Information" (about:support) page to go to the current Firefox profile folder or use the about:profiles page.

• Help -> Troubleshooting Information -> Profile Directory:
  Windows: Show Folder; Linux: Open Directory; Mac: Show in Finder
• http://kb.mozillazine.org/Profile_folder_-_Firefox

More information.

The following URLs bookmark fine:

https://philpapers.org/rec/HEPJSA?ref=mail

https://login.microsoftonline.com/login.srf?wa=wsignoutcleanup1.0&wreply=https%3a%2f%2flogin.microsoftonline.com%2fcommon%2foauth2%2flogoutredirect&id=501148

http://phdcomics.com/comics.php

https://tex.stackexchange.com/tags/accents/info

http://www.perseus.tufts.edu/hopper/

The following URLS do not bookmark:

http://ucelinks.cdlib.org:8888/sfx_local?id=10.1086/260376&sid=uchicago&date=1975&jtitle=Journal+of+Political+Economy&aulast=Whitaker&volume=83&atitle=John+Stuart+Mill%27s+Methodology&genre=article&spage=1033&issue=5&title=Journal+of+Political+Economy&issn=0022-3808&epage=1049

http://www.oxfordscholarship.com/view/10.1093/0198246420.001.0001/acprof-9780198246428-appendix-1

https://scanbot.io/en/confirmthanks.html

Please can you define what you mean by "Do not bookmark"?

How are you bookmarking these (as in, what actions do you take, what do you see)? When do you realise they aren't bookmarked?

Have you tried running the integrity check as suggested by cor-el?

Hi Standard8:

Thanks. When I did the Verify Integrity, I got the ability to bookmark back.

What I meant by "Do not bookmark" was that when I pressed CMD-D, nothing happened. I did not get an "Edit this bookmark" dialogue appearing.

So you know, the current Beta build of Firefox 64.0 is 64.0b7

Thanks!

The problem is back. Here's the Verify Integrity output. Any clues here?

> Task: checkIntegrity - Unable to check places.sqlite integrity: Error: Error(s) encountered during statement execution: database disk image is malformed > Task: invalidateCaches - The task queue was cleared by an error in another task. > Task: checkCoherence - The task queue was cleared by an error in another task. > Task: expire - The task queue was cleared by an error in another task. > Task: originFrecencyStats - The task queue was cleared by an error in another task. > Task: vacuum - The task queue was cleared by an error in another task. > Task: stats - The task queue was cleared by an error in another task. > Task: _refreshUI - The task queue was cleared by an error in another task.

Sorry for the delay, I've been ill this week.

"database disk image is malformed" means there's something wrong with the database and can't read it. Most likely something has caused corruption.

Firefox does its best to recover from it, but the fundamental reason needs to be looked at.

Do you know if you've been having any hard drive issues? or maybe crashes?

I hope you're feeling better now.

No, no "hard drive" crashes, as I have an SSD installed. I can print out a full system report and send it to you privately if you wish.

Update: I've now upgraded to 64.0b9 and bookmarking (CMD-D) is working again. Why don't we just wait a bit and see if things continue to work? If so, we can close the conversation.