We have found the root cause: Actually you are probably (by accident= executing a double click. As most of the area of the "Quit" button on the previous screen is in the same area as the "exit manual" line you quit the game.

Idea @Zeno: Ignore all left clicks for something like 500ms (or something like that) after returning from the manual screen. Maybe even for all screen changes. Whatever is easier. As a result nor more accidental double clicks should have any effect.

I actually tested it multiple times a single quick click in that portion of the screen will close the manual and then the game. It may be something that on effect certain OS (running windows 7) if you cannot duplicate it with a single click.

Fixed. This was actually caused by the fact that the mouse hack in the ASCII menus emitted the keypress on the mouse down event, and the graphical menus emitted the keypress on the mouse up event. So, mousedown closed the manual, and mouseup pressed the button in the main menu, which was already visible at that time. I have changed the mouse hack to also act on mouse up (and also changed the highlight to brighter while the mouse button is pressed).