I have exactly the same problem. When I look at the source code I see there the 2 sets of meta tags. One is the original and the second is Yoast created. In WP using Yoast the SEO shows as being correct but actually it is wrong because the search engines are reading the original set of meta tags.
After getting a green light for everything in WP SEO Yoast I ran Traffic Travis to double check the SEO and TT came up with a very different (bad) set of results. That is when I checked the source code. ??
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Is there a simple setting in WP SEO that we have all missed so that Yoast overrides the original <head> instead of appending it? Have we all missed something? Please help!
Could this be happening because I installed WP SEO Yoast after I had already created most of the pages on my site? If so, what should I do?
Thank you.