Sorry for the wishlist thing... I wasn't expecting replies to it. It was a rhetorical statement of wishes. (I don't expect a reply letter from Santa either.
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The window issue is not external-software related. Even the default "windows" capture, "The PrintScreen key", does not work. That captures windows screen-buffer, directly, and places the image into your clipboard. It captures everything except RenPy's screen, showing the windows behind it, or your desktop if you have no other windows open.
RenPy apps, all programs with a window, usually have a taskbar display. Unless it is in module-mode. (That is how we know programs are running, without going to the task-manager.) When you hold your mouse over, say... Chrome, it shows the page you are on, in chrome, when it is minimized or if it is behind another window. (Without dual displays, you never see it when in full-screen, because the taskbar is covered by the program, in most cases.) The screen for RenPy does not display there either, if it is fullscreen, non-windowed.
The chances that just RenPy is the only program that does this, and no other, and it is the drivers issue, is slim-to-none. This is all updated software and a standard Radeon-7970HD video-card, and the other was the built-in Intel-Display driver. None show the RenPy screen and none can capture a screen-shot from the program, when running in fullscreen non-windowed mode.
To test this... Launch a RenPy project. Set the display to "Fullscreen". Move your mouse to the other window's taskbar and hover your mouse over that games menubar, in the taskbar. (The tab with the same name as the game you just launched.) Should pop-up with a snapshot of the screen as you see it on the other monitor, or in the last state it was displayed, before being minimized.
Minimized, it displays a tiny black "X" or something where the thumbnail/snapshot of the screen should be, maximized, it displays... nothing, or a black box in the top left corner, or odd boxes all over, or solid black... depending where you are, in the game/novel. If you hover over the blankness... it should bring-up the screen, and show you that screen on top... Mine shows nothing.
Switch back to windowed, and now the taskbar menu shows the snapshot of the screen, and windows printscreen now works.
Like I said, it isn't a real issue. Few have dual-displays. Even less actually use screen-capture...
Same with the mouse... But even in a visual-novel, your hand can "drift" the mouse off the screen, and end-up clicking out onto your second desktop, hitting icons, launching other programs. (If you have a desktop like mine, where my icons run off both my screens, into purgatory... That happens a lot! Happens more when I do visual novels, because I am usually focusing on reading and clicking, not holding my hand steady and re-positioning my mouse every time I click.)
Going to be remapping that "S" key to "WASD" movement/input anyways... Why is it not a standard key, like "Print Screen", or "F12"? Just curious... No reply actually needed.