I think I know where it is coming from; in
JavaScript:
Window_TimeOfDay.prototype.initialize = function (x, y, width, height) {
width = 150;
height = 65;
Window_Base.prototype.initialize.call(this, Graphics.boxWidth - width, 0, width, height);
this.setBackgroundType(0);
};
For some reason, the window isn't hidden when it is initialized, only on the first update, so that's may be the cause.
Try to code the following code to this method:
JavaScript:
this.visible = $gameVariables._clShowTimeWindow;
If it solves the issue, I will add it on the github.