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.

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Cheers,
Paul Edstein
[Fmr MS MVP - Word]

yes, definitely using the journal's Word template which was written on a version before this change. I'll play around with a fresh doc and no old templates and see if the behavior changes, and more importantly if there exists a way to include the endnotes in the main column balancing.

unfortunately I have to change it to match what the conference proceedings wants, which is 2 column and references at the end of the last column, not in a new section of columns (or a single column). needs to be in two columns like in the first image. i did put the REFERENCES title back in as a separator instead of the last main body item before the separator, but no separation/continuation lines, etc. if it was a journal I could just ask the copy-editing staff to fix it after submission, but not the case here.

If there's no way to get that result anymore in MS word, I'll need to ask the conf paper staff what they suggest. or go to latex