I've looked at the configuration, and almost everything is correct, except 1 thing. On the General Options -> Sources 2 panel you had the portfolio categories selected. If you look at the option name it says “Return taxonomy terms as results”. That means the search returned the taxonomy terms as well as the portfolio items.
The reason why you got results even if all the check-boxes were disabled, is because the taxonomy term results are not affected by the taxonomy term checkboxes, because they are one and the same thing.Best,
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