I am having similar problems trying to connect to a domain controller that is not a global catalog. However, I am using ArcGIS for server version 10.3.1. My error message reads:
"Could not connect to the identity store as one or more of the connection parameters is incorrect. Verify that you can connect to the identity store outside of ArcGIS Server using the same parameters. [IP Address]:3268"
Essentially I think the issue is (as previously mentioned) that it is trying to connect on port 3268 which is only for global catalogs. However, updating the config file (as per the link, or the 10.3 link http://server.arcgis.com/en/server/latest/administer/windows/configuring-the-domain-controller-used-...) does not resolve this issue.
I also tried adding ":389" in the configuration but this threw an even uglier error message when I tried to retrieve the users.
Does anyone have a 10.3.1 workaround for this?