I am not certain what exactly this message means. If you look in the "error log" view within the Console does this report any additional information?
I forgot I'd put this message here. I ended up raising a support ticket about the problem in the end, but the issue was resolved by simply shutting down the Server Automation Console and starting it up again lol... I probably should have tried that myself
It was something screwy with eclipse that was causing it I believe, but the problem went away after restarting the console GUI.