Firefox does not save changes to options when starting it up anew; I have to go in and re-change everything on start-up every time.
Every time I start Waterfox anew, it resets all my settings to what they were when I first got it. I tried uninstalling and reinstalling, but that didn't work either. It doesn't even keep my preference for what shows up on start-up; it just shows me the Waterfox start page and the "your browser has been updated" page.
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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 think Waterfox uses a similar kind of settings storage as Firefox, so check out this article for suggested things to investigate: How to fix preferences that won't save.
Also be aware that external programs like Advanced SystemCare may block unwanted changes by rolling back to an earlier saved settings file between sessions. This kind of "Surfing Protection" or "Browser Protection" or "Home Page Protection" feature should be disabled until your settings are perfect and only then would you consider enabling it. (Making regular backups and avoiding malware are probably more useful!)