You need to break the LinkToPrevious in your new section. Here's code I am using to do something similar (I am also clearing all text as well). Be sure to set the 'sec' variable to your newly created section to use this:
Code:
For i = 1 To sec.Headers.Count
' Unlink Header from previous
sec.Headers(i).LinkToPrevious = False
' Clear header text
sec.Headers(i).Range.Delete
Next i
For i = 1 To sec.Footers.Count
' Unlink Footer from Previous
sec.Footers(i).LinkToPrevious = False
' Clear footer text
sec.Footers(i).Range.Delete
Next I