I have linked my GA account to my Webmaster Tools account, so I'm getting access to the Search Engine Optmization -> Queries report. But the top query listed in that report is (not set).
Note: this is NOT (not provided) -- it's (not set). Also, I have linked my Adwords account to GA as well. And I'm using Universal Analytics
This (not set) item currently represents 42% of impressions and 52% of clicks.
I saw this post here, which says that (not set) means these people came to my site directly:
However, if that's the case, then howcome (not set) shows values for clicks, average position, and CTR?
I am seeing thousands of other queries in my list, but having 52% of clicks invisible to me is kind of annoying. Is there something I'm doing wrong? Or is this just data that's not accessible to me, for some unknown reason?