that setting is stored in two different places :
in the settings file (like other settings) and in the meta.xml file (used at boot).
Maybe your meta.xml file is write protected, or the data inside is not good so the loader couldn't edit the info.
try restoring the original meta.xml in your loader's folder (link in my signature, or on official website), or edit the meta.xml yourself manually by removing the commented lines and editing the argument to disable auto mount usb.