Are you running an addin which enforces document classification? Where I work, we have a tool (Boldon James - Email and Office Classifier) which requires every document to show a classification tag. The behaviour you describe sounds suspiciously similar to how that tool works. I would assume there are other tools that work the same way.

Our tool is customised by our IT group to allow us to set the classification to 'Manually Marked' which prevents the tool from changing the header/footer. The tool adds a ribbon customisation to the Home tab where we can select a classification and when the document is saved that setting is applied to header/footers according to the configuration settings.

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Andrew Lockton
Chrysalis Design, Melbourne Australia