Your note that it appears to be version specific made me go back to your original file to do some testing. If I convert your document to a specific version I can see that your preferred behaviour occurs shows up in file formats Word 2007 and 2010 but not in later versions.

Open your vba editor's Immediate window and type the following line and then press Enter
ActiveDocument.SetCompatibilityMode wdWord2010



You should see that the footnotes now line up with their respective columns.

The same thing happens if you try
ActiveDocument.SetCompatibilityMode wdWord2007

However this one goes to the 'load balancing' version that you don't like
ActiveDocument.SetCompatibilityMode wdWord2013

__________________
Andrew Lockton
Chrysalis Design, Melbourne Australia