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Google Analytics - (not set) where I've never seen it before.

Aquisition > SEO > Queries

     
7:27 am on Oct 1, 2015 (gmt 0)

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I'm doing an assessment on a website where I have Analytics data going back a while, but where it was only registered with WMT/GSC 10 days ago and I just synced that with Analytics today.

In Acquisition > Search Engine Optimisation > Queries I'm seeing the second most popular query as (not set) - that's 25% of impressions and 22% of clicks. When I compare in WMT/GSC I don't see this.

There are (not set) keywords every day of the 10 days I have data for and they are from all over the world. As WMT/GSC and Analytics NEVER agree I can't do any more meaningful comparisons.

I've never seen this before and I've just checked the two busiest sites I run to see if the problem is happening on their latest data - it's not. Not one (not set) keyword.

Anyone else ever seen this? Any ideas what it could mean? They are not running AdWords or Google Display Ads.