Usually you are only prompted to load UI settings if a file doesn't exist already.
And as for my included layouts, they are a bit dated and I apologies for keeping them in there as outdated files. I'll try to submit some more up-to-date layouts that might be a bit more common for users.
On a final note, my UI isn't really designed to fit together like a full game interface. Since most windows are free floating, it's just like a doctored up Default UI, free for the user to create their own preferred layout.
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