The Word 2013 behaviour varies according to whether the document is based on a Word 2010 or earlier template, or a Word 2013 template. I suspect your Save As caused it to switch to the Word 2013 template. The only thing I'd be inclined to change re the 2nd representation of your document would be to insert continuous Section breaks either side of your 'References' heading and formatting that with a single column layout, so there's a more obvious break in the text flow.

__________________
Cheers,
Paul Edstein
[Fmr MS MVP - Word]