If these boxes' you're referring to are just ordinary textboxes and/or table cells, the behaviour is by design. The only way such features can be accessed once 'filling in forms' protection is applied is by putting Section breaks either side of them and leaving the Sections containing the ordinary textboxes and/or table cells unprotected when applying the 'filling in forms' protection.

The other possibility is that whoever designed the form used a mix of content controls and formfields. These were never designed to work together and problems such as you describe are typical in that scenario. Moreover, content controls don't work properly on Macs and ActiveX controls (just in case those have been used) don't work at all on Macs.

Anyone designing forms for Macs should know all this.

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Cheers,
Paul Edstein
[Fmr MS MVP - Word]