On Win 7 64 bit Firefox, 15, 16 and 17 beta will not save "Options" settings.
I keep up with MS and Mozilla updates. I do not remember other significant event which might have caused this problem. The advice in "http://support.mozilla.org/en-US/kb/how-to-fix-preferences-wont-save" did not help.
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Some more testing. Running Ff 17 Win 7. The initial response to this problem told me to delete the prefs.js files (and some similar) from my Firefox profiles. Having done that I restarted Firefox, updated my start page preference and "save downloads to" option. After a Firefox restart the "start home page" had not been saved but the download save option had. Looking at preferences saved in my profile prefs.js was empty and prefs_temp.js was full of data. So I started Firefox, updated my "start home page", looked at prefs_temp.js and it contained my updated home page option. I shutdown Firefox, checked that my update was still in prefs_temp.js, copied my prefs_temp.js to prefs.js and resterted Firefox. Square 1, the default home page displayed, not my update.
Did you try to delete both prefs files to make sure that they weren't locked or otherwise protected by security software (firewall, anti-virus)?
You can check for problems with preferences and try to rename or delete the prefs.js file and possible numbered prefs-##.js files and a possible user.js file.