I looked into both of those solutions and neither of them are the case. There are no missing paragraph marks as far as I can tell. The anchors are not miss-positioned and are anchored to the page, not to a disappearing merge field. Furthermore, I attempted to group the objects with objects that remained in the header and footer. When I did that, all of the objects I grouped disappeared. When printing however, all of the objects are visible.

I don't understand - are you saying they disappeared from view in the mailmerge output file, but printed anyway?

It would be easier to diagnose the issue if you could attach copies of the mailmerge main document and an output document to a post with some representative data (delete anything sensitive). You do this via the paperclip symbol on the 'Go Advanced' tab at the bottom of this screen.

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Cheers,
Paul Edstein
[Fmr MS MVP - Word]