Your description suggests one or more sections have a 'different first page' layout. In that case, a header on the first page of that Section wouldn't be carried through to subsequent pages. The other possibility is that you have multiple Sections whose headers are not configured 'same as previous', and that the one where the header re-appears was originally linked before being unlinked to enable a new Section to be inserted. Setting all headers to 'same as previous' should resolve that issue.

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Cheers,
Paul Edstein
[Fmr MS MVP - Word]