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.