This seems like a bug because the exact same functionality exists in MS Word 2007 and I can make it work in MS Word 2007. And if I open a file I create in MS Word in Atlantis, Atlantis changes the endnote numbering to continuous and nothing I do will change it back.
Anyone know if this is an issue? I am using version 1.6.5.1.
Please choose the "Insert | Footnote..." menu command of Atlantis, and click the "Location > Endnotes" box at the top of the dialog. Does the "Numbering" box at the bottom say "Restart each section"?
Is the "View | Print Layout" menu command checked in your Atlantis?