Found the answer! In %appdata%\Roaming\Remote Utilities Files is an XML called "connections.xml" or similar, and in this is a complete list of all connections in XML format. There were several entries that weren't showing up in RUT viewer, I deleted these and all is good again!
I can't connect to any of my connections because apparently "My license does not allow using this key for more than 10 computers" - yet I only have 8 connections. How can I get this working? I had 10, yesterday added a new one and got the message, then I removed 3 old unused connections but still getting this error.