Settings won't save in Firefox

This is another common problem I see in forums lately. This especially since more and more malware targets firefox as well.
An example we see in forums lately is "Yoog Search". This is a searchengine Hijacker - comes with a variant of AdRotator/IconAds Adware.
The Firefox startpage + searchengine / Searchsettings get hijacked and even though the malware (responsible for changing startpage+searchengine) is gone/deleted already, if people want to change it back to default again, or change it back to their own startpage / searchengine, firefox won't save the settings.
So after a next Firefox session, the Hijacked startpage / searchengine etc is back again.

The cause is a user.js file present inside the Firefox profile folder. So, in this case the %APPDATA%\Mozilla\Firefox\Profiles\"identity" folder.
The user.js file does not exist by default and was in this case added/modified by malware.
This file is used to set or reset preferences to a default value. For example whenever the browser is loaded, the values present in the user.js file will supersede the stored values in the prefs.js file.
The prefs.js file contains the values you can access/modify via about:config or via the preferences in Tools > Options Menu in Firefox.
See here for more info about the user.js file.

I've also seen the same where malware changed the Proxysettings and created a user.js file to store the Proxysettings there. Result > once the malware was removed, the user would get the error: "The Proxy Server is Refusing Connections" since the user.js file is still in use.
Some versions of the Ask Toolbar also create a user.js file in the Firefox userprofile, so after uninstalling the Ask Toolbar, the homepage + searches are still set to Ask.com because the user.js file is still present.

That's why, if you're ever having problems with Firefox that won't save settings like startpage, searchengine, proxysettings etc.., then look if a user.js file is present in the Firefox profile folder and delete or modify it.
The presence of user.js in the Firefox profile folder doesn't necessarily mean that it's a bad file. Many people create their own user.js to supersede the stored values in the prefs.js file. So if you didn't create the user.js file yourself, you may delete it (since it's not present by default anyway).
If you're not sure, just rename it to user.js.bak, or open the file with notepad to see what values are present there.