Sadly, no there's no way to edit the server_settings.ini. If you have the bug, your only option is to replace the file with an unbugged version and reposition your windows.
Window Settings --)> Default Location should place the window in the lower right corner and MIGHT fix the save problem. If it doesn't go to the lower right corner, you've got something else going on.
The Doc file included in the ZIP has instructions for setting Dock as the default.
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