I had the issue once, delete the GCpad.ini and everything worked. In 4.x the GCpad.ini is in the users folders.
C:\Users\Administrator\Documents\Dolphin Emulator\Config
Replace administrator with your user name.
C:\Users\Administrator\Documents\Dolphin Emulator\Config
Replace administrator with your user name.
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Working controllers
[url=http://spreadsheets.google.com/pub?key=tGD-U_eW1Rc7rNyqkpgJuIg&output=html][/url]