I have noticed for a while now, when I upload a sketch from arduino through the little teensy uploader applet, it has to be at least partially visible on the screen to complete the upload, otherwise arduino IDE gives an error that the teensy failed to respond.

Would it be difficult to make this work regardless of the teensy uploader visibility on screen? Alternately, maybe the window could be set to "always on top" or have a menu option to set as such? I mainly bring it up because often the sketch window ends up on top and I hit upload, wait, and error unless I immediately hit command tab to flip to teensy or move my sketch window etc.. and while I have adjusted, it could be a bit confusing for a beginner.

Out of curiosity, what is the reason this external uploader is required? Is it mainly for copy protection to secure the bootloader? or is there something about arduino IDE that doesn't allow a critical element of the upload process?