I found it easier to hardcode this. Open the file sites/all/libraries/ckeditor/ckeditor.js in Notepad++ Go to line 22 or search for shiftEnterMode
Change following:
enterMode:1,forceEnterMode:false,shiftEnterMode:2,
into:
enterMode:2,forceEnterMode:false,shiftEnterMode:1,
done!