It seems WinMerge is not saving the Location Pane settings.
The work around is to edit the registry setting for WinMerge.
HKEY_CURRENT_USER\Software\Thingamahoochie\WinMerge\Settings-Bar0\Visible = 1
Set Bar0 Visible to 1. May have to close and reopen the Registry Editor to save the new setting.
The same might happen to Diff Pane. Use the registry setting below.
HKEY_CURRENT_USER\Software\Thingamahoochie\WinMerge\Settings-Bar1\Visible = 1 (Using "Settings-Bar1" instead of "Settings-Bar0").