There must be a setting file which it's seeing when launched from the GUI. See if there is a settings file which you don't end up accessing in the case where you launch from command line. Perhaps when you launch from the command line either; you're doing so from an environment or directory where the settings file is inaccessible, or perhaps you're giving it arguments which cause it to override defaults or configuration loaded from a settings file. But when you launch from the GUI, it uses the settings file, because it happens to be accessible and there. That's just a possibility; I don't know the answer for sure.
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