To clarify what Tatsumaro said, here is
a post showing a template of what the parts of window.png are. You need to put an opaque color in the "Body" section.
However, that alone isn't sufficient to make the window background opaque, because by default the opacity of the windows is 192 (out of 255).
To get the window truly opaque, you also need to edit your project's \js\rpg_windows.js file. You need to find this function:
Code:
Window_Base.prototype.standardBackOpacity = function() {
return 192;
};
And change it to this:
Code:
Window_Base.prototype.standardBackOpacity = function() {
return 255;
};