Ah yep now I understand what you mean, thanks for being so thorough :)
You are correct, the menus/buttons, etc are only clickable while the Desktop Buddy application is the active "window", so it will become passive/unclickable when you click on anything else, and then will only become clickable again when you activate it by clicking on it in the Taskbar or by alt-tabbing to it.
I'm working on a solution for this issue, as yes it is, as you said, not intuitive as it currently stands. I'm just trying to find the right balance of maintaining interactivity with the Decker avatar while still allowing the user to go about their business and not be hindered or encumbered by Decker being on the desktop. I accepted the current approach for now, as it gives the user full control of when Decker is intractable and when he isn't, as he is designed to be a background application first and foremost. Being in view, but not "in the way" as much as possible. You can see the dilemma here.
Thanks again for your feedback :)