I'm also having the same problem with a refurbished controller I got a few weeks ago. Trying to play Skyward Sword but the controls are backward. I swing down and link swings up, left and he swings right etc. I found 2 other people with the same problem here and here. I sent in an email last week but haven't heard anything back yet... hopefully we can get some help here. Probably just end up calling customer service.
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