The Differences window is always the top most window on my desktop and is above all other windows
You have the option "Keep window on top of all others" enabled on the Differences window. If you do not want this, then when the Differences window is next displayed, click the roll-out bar at the top of the Differences windows (where is says "Click here to see more options"), and untick the checkbox "Keep window on top of all others". The setting will take effect the next time the Differences window for that profile is displayed. Note that this setting is not global, it is a per-profile setting.