Wayne, I did a quick test with the extension you mentioned and I didn't run into any issues. How are you setting the configuration table? The way I did is run 'GetConfigurationTable', give my 'QueueName' a new value and then set it via 'SetConfigurationTable' with persistent set to true.
Of course, if you are actively editing the Thing or have the Thing open, you would need to hit Cancel Edit or close the Thing and reopen to see the changes. Updating should not cause the Thing to stop running though.
You pointed out something that should have been completely obvious. While we were trying to get this to work, the thing which we were trying to update was open in editing mode. Once you pointed that it, it made perfect sense. Unfortunately, I'm not onsite with my client anymore to personally verify, but I have asked them to test and let me know. Hopefully, it really was as simple fix as you pointed out.