Well, I'm still not positive I even know what you're asking for. It sounds to me like you're saying that when you open a new scene the text window is still open and it blocks some of the scene. That's kind of what it means when you say it isn't disposed. If you're not using any scripts, then that's impossible...
So maybe all you mean is that when it takes a screencap for the background of a scene, the text window is still open and so that forms part of the background? Is that yout problem? If so, just put a wait event command right before calling the new scene.