Your System Details shows you are using Firefox 53 beta. Is this correct?

Profile data can be removed or not recorded several ways;

• 1) Running Firefox in Private Mode (nothing is recorded)
• 2) Privacy settings; (In the address bar, type about:preferences#privacy<enter>)
• 3) Many disk cleaners and anti-virus type programs can remove data from browsers. Open their settings and have them leave the browsers alone.
• 4) Mal-ware.

https://support.mozilla.org/en-US/kb/how-to-fix-preferences-wont-save

Note: Some software, like Advanced SystemCare with Surfing Protection, can protect files in the Firefox profile folder against changes. If you have such software then check the settings or uninstall this software.

I'm running Firefox on Debian Testing (About Firefox tells me I'm running 53.0 (64-bit) )

Regarding the points: 1) No, I'm running firefox in normal mode. 2) Privacy-Settings are set to "Remember History" 3) I don't use any diskcleaners or anti virus software 4) Seems very unlikely

I don't know where and how the password exceptions are stored I've found a File in the Profile-Folder called "notificationstore.json" which is very likely the file where firefox stores the notification settings, but I don't know the syntax, otherwise I'd have tried out what happens if I manually add sites there

In case you use "Clear history when Firefox closes" or otherwise clear history.

• do not clear the Site Preferences

• Options/Preferences -> Privacy & Security -> Firefox will: "Use custom settings for history": [X] "Clear history when Firefox closes" -> Settings
• https://support.mozilla.org/en-US/kb/delete-browsing-search-download-history-firefox

• clearing "Site Preferences" clears exceptions for cookies, images, pop-up windows, and software installation and exception for password and other website specific data
• clearing "Cookies" will remove all selected cookies including cookies with an "Allow" exception you may want to keep

@cor-el: I already wrote: I don't use "Use custom settings for history" nor "Never remember history". My privacy setting is set to "Remember History"

I've tried to set it to "Custom" and made sure "Clear history when Firefox closes" was unchecked.

Do you keep other Site Preferences like cookie exceptions?

The password exception are stored in logins.json along side with the encrypt usernames and passwords under "disabledHosts" at the end of the file.

Do you have a problem with storing a new password?

Note that Firefox 58+ is using logins.json and key4.db (previously logins.json and key3.db).

I've checked my .mozilla folder and haven't found a logins.json. It was there when I first saved a login.

I've also tried to manually add a site where I don't want my passwords to be saved but it was ignored.

When I go to the exception list in the preferences page I see the saved exceptions of this session, but not the one I manually added nor the ones I added in sessions before.

Are other files in the profile folder updated when you close Firefox?

Note that Firefox uses two locations for the profile folder, so make sure that the read/write permissions are OK. You can find buttons on the about:profiles page to go to both locations (root and local).

• http://kb.mozillazine.org/Profile_folder_-_Firefox

Also check the settings for "Clear history when Firefox closes" to see if passwords are possibly included.