It seems that the messagewindow in CLI Script doesn't have mousescrolling whether it is focused or not.
Scrolling with the mouse seems to work everywhere except that window.
Using the scrollbars works though.
To replicate, execute this jscript code, then try to scroll the output by using the mouse.
for (var i=0;i<50;i++){
DOpus.Output("HELLO "+i);
}