You may have missed some of the sections, which you can easily do for sections that are limited to part of a page. Display the section number on the status bar and carefully check that you change the restart option for all individual sections. Alternatively,
you can run the following macro:
Sub NotRestartPageNums()
Dim s As Section
For Each s In ActiveDocument.Sections
s.Footers(wdHeaderFooterPrimary).PageNumbers _
.RestartNumberingAtSection = False
Next s
End Sub
See
http://www.gmayor.com/installing_macro.htm.