I have the same issue. I checked and Dolphin 4.0.2 (stable) has all the options, but this does not seem to apply to the version I am currently using, 4.0-7021. Dolphin recognizes my controller and I can configure it under 'Controllers' -> 'Configure', but I can't select a Pad number in there and I don't see any 'Port' options in the 'Options' -> 'Configure...' -> 'GameCube' tab. 

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OP: