This issue had us puzzled for weeks. The issue was that whenever we changed anything on one of our Agent Builder Agent even though the TEP support was correctly installed and the new support files downloaded by the TEP javaws client the views were still messed up, wrong order, incorrect titles, etc. The problem was still around after stopping the agent, clearing offline entry and starting the agent and getting it again into TEP. Just like this agent here:

We figured out that the issue is basically that the agent has to be cleared out from EVERY navigator view where it is present. For some reason it is not enough to clear the offline entry from the Physical view you have to delete them from all views. After the agent is gone from all views in question do the following:

Restart the agent from TEP.

Wait until the agent greys out on the console, then select Clear offline entry from the dropdown menu. The agent will now be gone from the Physical view.

Once the agent has been restarted, it pops back in to the TEP console but now with the correct views and workspaces. Now all you have to do is to assign the agent back to its navigator views.

We can summarize that the whole problem was because the agent was present in multiple navigator views…