OK, I'm back as the problem persists. There are a couple of problems but I will focus on the first error instance alone for simplicity sake (Table of Contents and the chapter that follows).

As I say, this macro creates a book, each Section being a chapter. The Cover Page is created without issue. The Table of Contents is always next and is inserted as described above (it's essentially a blank page). The header and footer are created without issue. A Section Break (Next Page) is inserted and that creates the same header/footer (Table of Contents) in the new section (I'll call this Section, the 3rd, "Site Data"). The 2nd and 3rd Sections are pretty much identical at this point.

The next chapter is almost always the same. This chapter is not inserted as a blank page but is "built" on the page created by the Section Break. It starts out like so:
Documents(FullDoc).ActivateActiveDocument.Paragraphs.Last.Range.Select
Selection.End = Selection.End - 1
'Configure First Page Header/Footer while on the first page
Selection.InsertBreak (2)
Selection.Bookmarks.Add "InsertionPoint"
ActiveDocument.Sections.Last.PageSetup.DifferentFirstPageHeaderFooter = True
Call Copy_And_Paste_To_Compilation.Turn_Off_Link_To_Previous 'Turns off LinkToPrevious
This is where things get weird. Here is the code:

Sub Turn_Off_Link_To_Previous()
    Dim HdFt As HeaderFooter
        For Each HdFt In ActiveDocument.Sections.Last.Headers
            With HdFt
                .LinkToPrevious = False
                .PageNumbers.RestartNumberingAtSection = True
            End With
        Next
        For Each HdFt In ActiveDocument.Sections.Last.Footers
            With HdFt
                .LinkToPrevious = False
                .PageNumbers.RestartNumberingAtSection = True
            End With
        Next
End Sub
If I step through, the code executes as it should without altering anything but setting LinkToPrevious = False. However, when I run the code full speed, it deletes both the 2nd Section's header and footer (Table of Contents). It also restores the 2nd Section's setting LinkToPrevious = True. It also deletes the 3rd Section's ("Site Data") header and footer which at this point is a repeat of the 2nd Section's header and footer (Table of Contents). Also, the 3rd Section's LinkToPrevious setting is also set to True (after just having been set to false?).

Every time I step through it, it executes properly. Every time I run it at full speed, it errors as described above.

I don't get it. I can't imagine what might cause it to behave this way.