So you are trying to publish from ArcMap to ArcGIS Server, and you are getting "The server is not ready for publishing. Please check if the Publishing Tools on the server (System/PublishingTools) are started."
You've checked the server in ArcGIS Server /arcgis/manager => services/system and the publishing tools are not secured, and the system folder is not secured. (if not, try that too, some people say marking it secured and then unsecuring it again can clear out some resident issues).
Maybe you also checked your ssl settings, went into IIS and exported your certificate with a password, went back into https://server:6443/arcgis/admin/machines/servername, sslcertificates, and imported the saved cert, then backed out and put the common name in under the servername settings? Go do that too, if your webadaptor resides on the same server as arcgis server. If you don't, ssl errors may stop the publishing behind the scenes.
But publishing as a windows active directory account still won't publish. You tried publishing through the primary server account and that doesn't work... unless you specify the port and avoid using the web adaptor?
Then this may be your issue.
On the server with the webadaptor on IIS, try to browse to https://yourserver/arcgis/admin/machines/ and click yourservername.domain.com. Did you get a URLSCAN rejection?
- Go to Windows\system32\inetsrv\urlscan\urlscan.ini
- Set AllowDotInPath=1, then save the file.
- Find the section for [DenyExtensions] where it says ; Deny executables that could run on the server. Put a semicolon in front of the line that says .com.
- In CMD prompt, type IISRESET
Now you should be able to publish through your webadaptor using windows active directory accounts that are part of an authorized domain group with "publisher" role assigned in the server/manager roles page.
Hope this helps someone!