I found an old question asking exactly the same problem I'm experiencing. http://community.kaseya.com/xsp/f/114/t/11746.aspx
I have the same kind of issue, I've created different Machine Groups and got two of our file servers in the wrong one. In the Manage Agents section I can check the two file servers, click on Manage > Change Group and then select the correct Machine Group from the drop down. if I reload the Manage Agents section the two file servers show back up in the incorrect Group ID. If I just refresh the list it'll show the correct Group ID. I went as far as uninstalling the Agent (uninstall at next check in) and then re-installing the agent with the Agent installer for the group I want the file servers in but no change.
Trevor, I'd check the "Naming Policy" section under System->System Preferences. My guess would be that you've got a connection gateway and IP range rule in there that keeps moving them back into that "incorrect' group.
That did it, my boss had originally set up the org and I've never gone into that section of Kaseya to make changes. One more problem solved!