The ID had letters and numbers starting with V. The ID shown didn't match any of my numerical ID's so I had a big wtf moment.
This is the Viewer ID. The Active tab in the admin console shows Viewers and Hosts that are currently using this server for a remote session. Please refer to this article for more information.
So it was appearing under Active when it wasn't working and it's no longer appearing when it really is working. That's just backwards
Unfortunately, we couldn't reproduce the issue. However, we plan to release a newer version of Remote Utilities later today. Please try updating Host, Viewer and RU Server once the updated version is out and see if the problem persists.
Could you please clarify if you mean the First connection warning? This warning is shown only once and it goes away when the remote user clicks on it. However, it doesn't affect your ability to connect right away, it's an informational message. That message is necessary to let the user know that the program was installed and to prevent the rogue activities out-of-the-box. Remote users must always know that they are being monitored or are about to be monitored.
Unfortunately, there is no possibility to minimize the Agent to the tray. The Agent is supposed to work explicitly, that is it should always be visible in the taskbar. If we add a tray-only option the remote user may easily overlook the fact that the Agent is running on their PC.
I am sorry if that makes the program less useful for you.