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I would bet that it is an app causing your issue,the deep sleep function doesnt block rogue apps from periodically trying to wake to update or access certain gps location etc.

I would use titanium backup and the freeze app function to isolate the app or you can do a clean install and slowly reinstall the apps until you find which one is doing it. I had similar issues that were caused by the facebook app months ago,not sure if it still causes issues though.
 
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