There doesn't seem to be many other results for a google search on this error, so in case anyone else encounters it, it may be useful to add some more info to this page.
I encountered what seems like a very similar error and had to work through a few different issues before i was able to join new my new server to my site.
Firstly, I had forgotten to install a 64 bit oracle client, so while tnsping etc worked perfectly, arcgis server didn't have a chance.
Then after installing a 64 bit instant client and configuring tns_admin and path environment variables, the number of connections listed in the error fell from 6 (ie all the oracle connections in my site) to just one, and that one remaining problematic connection happened to be the one that has an unrelated intermittent network issue, which I verified with a basic ping test .
So finally, after dealing with the underlying network issue, I could then join my server to the site. And none of this had anything to do with the account being used to run arcgis server or the read/write permissions on the connection files.
