I saw your video. Is strange when I am typing "z" in my Application Game Kit Studio 0.49b the "z" key works. Also in your video your "z" worked and not worked too. Maybe is a keyboard issue or maybe you have some program which interacts with the "z" or something. Or virus?
About the window disappearance I haven't replicated the bug in my computer yet. I tried to open many projects too and many source code windows too.
How much memory RAM do you have?
Sometimes windows when they don't have much memory prevent to open some windows to avoid the computer crash.
Just to say restart your computer maybe will not solve your problem. But test the same you did in a different computer maybe solve the problem. Or you will see if the problem is with your computer.
I am using windows 7 here. Maybe you are using Windows 7 too, because I see the Aero Window theme which is from Windows 7 too.