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I'm seeing some of the same things. What I think analytics is not counting, at least for me, is image search traffic. For example I have one blog that gets around 2,000 uniques a day. about 1,800 of those are from SE's. My server stats still shows around 2K a day, but analytics only shows getting around 1500 a day and it shows nothing from google images (where most of the image traffic is coming from.) I'm not sure why that is.
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