I had a scenario where the remote server config failed as I put the wrong IP address as the source server for system databases.  I corrected the issue but it would still fail if I re-ran the setup.  I worked out that it was the copying of the server ID file which was causing the issue as I was copying it from a network share to the data folder.  The first time I ran the setup the ID file was copied without issue but when I ran the setup again it failed at this point as the ID file was already in the data folder.  Changed the setup config to use the ID in the data folder and it finished without a problem.

As with D Porter, I have seen setup fail when there was issue reaching the source server for system databases. In my case, the network connection between the remote server and the administration server of the domain that I was trying to pull system databases from was slow and unreliable, and network timeouts were interrupting the install. My solution was to rerun the install, and choose a server on a different network segment to pull system databases from.

Through Navigatori I went to the server.ID and Properties -> Security Tab. Changed the User ID and Primary Group ID to "Use Current Thread"

Thanks to all who helped