maybe you have not correct permissions in your settings folder? if you do your overrides throug admin you need to give the user running apache (or web server you have chosen) the rights to right in your settings/siteaccess/whatever/override.ini.append.php file.
I'm talking about chmod or chown commands. if you want to change settings through admin interface, you will probably need to chmod 777 your settings/siteaccess folder, or maybe chown www-data:www-data that folder, being www-data the user running apache (debian, ubuntu default i think)
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