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, untick the option 'Keep window on top of all others' from Display menu (on the top of Differences Window). 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.