The problem described above is a bug in the UIBuilder. When the display is in Run mode (Play button pushed), trying to move a window, will resize the entire section (ie MainHUD), giving it really odd properties. Thus, everything disappears.
For now, just turn Run mode off, and to move a window around, you have to click the top most element in the tree (the window name itself) and then click and drag the box (without clicking on another element).
Also, to hide all the other windows, you just have to select them all in the tree window, and hide them with the eye-looking button.
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