And make sure you're using the Google API key in WP - if not, they may be sending you data which would make WP show your rankings as "unlisted", etc., when in fact, they're just penalizing.
There was problems with abuse of the Google database by WP users a couple of years ago, and Google's answer was to "penalize" sites abusing Google's database by over-querying through WP.
I'm sure this would apply to any software tool and over-use, just that WP was the one made an example of & got talked about.
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