Well, first, the UI settings are separate from the UI. With those settings in eq2.ini you'll always use ProfitUI. When you're offered the option of loading the UI settings from an existing character, all that does is load window positions and sizes and the like. If the UI settings came from a different UI (say the character's UI was arranged using the default UI but you're now running ProfitUI), window positions will be weird. You should also see a number of UI settings for the ProfitUI server for characters corresponding to various screen resolutions. Those are Profit's default UI layouts for different screen sizes.
/loadui is a command you shouldn't use. It doesn't load the UI settings, it reloads the underlying UI XML. It's notoriously buggy and doesn't initialize everything completely, basically if you aren't a UI developer you probably shouldn't be using it.
As far as the ProfitUI updater vs. zip file, the updater always has the most current files on it. The zip file is only rebuilt intermittently, so it's almost always out-of-date. Generally you want to use the updater so you get the current files with all the bug-fixes and updates to match changes in the game.
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