You are using legacy checkboxes and formfields with new content controls which are not designed to work in protected documents. I'm surprised you got it to work as well as you did. (You can have both in the same document, but not in the same section.) My advice is to use either all legacy fields (formfields and checkboxes) in a protected document or all content controls in an unprotected document.

See Content Controls Custom Checkboxes. This page has an Add-In you can download to put checkbox content controls in a Word 2007 document. However, all users of the form must have the Add-In installed.