Chickenjedi, you've answered my question too. My guitar was displaying the exact symptoms you'd described, relatively tuned at the 5th sounded fine, as soon as I held a chord it was like Les Dawson took a hold. It sounded terrible. So do I simply listen to how the note sounds in order to get it right at the 12th? Or is there a note I am looking for and will my electronic tuner be of use?
P.S. For those who have never seen Les Dawson, try here... http://www.youtube.com/watch?v=iZh8LJOy4xI