One way is to press the up arrow in the command window so the history shows up. Then you can right click the bar on the top of the history popup window and choose to dock the window.
That should solve any annoyance with the default behavior.
Also, to change it back or open it if it is closed you can go to:
Home Tab > Environment Section > Layout > Command History
and choose docked, popup, or closed. (The section names are at the bottom of the tab area.)