I just ran into this same issue and after working through re-installing web adaptor several times, checking file permissions, changing certificates, the solution ended up being something simple. I called Tech Support and was able to get it resolved quickly. When creating the binding on my certificate, I had entered the Host Name. For some reason this was causing the web adaptor to not be able to configure the Portal while Server was still fine. Whenever this was left blank I was able to configure web adaptor right away. Hope this helps with future configurations.
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