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The only thing that seemed to work for me is a full restore of my iPad. After that, the clock was aligned correctly.
 
Hmm. I hadn't noticed this until I saw this thread, but indeed my wi-fi only 64GB iPad Air 2 clock is 163 seconds fast. My iPhone 6 clock is essentially dead-on. Both are running iOS 9.1 developer beta.
 
My iPad Air 2 is -.806. My iPhone 6 is +.014. So almost 1 second difference between the two.
 
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