Hello,
Maybe the DOCX is using a style name that requires setting the enforceSectionPageBreak option as true (we recommend you to enable this option in mergeDocx and try again) or it uses a not supported style. The current testing version of phpdocx includes some improvements when working with mixed numbering styles in custom paragraph styles. Please send to contact[at]phpdocx.com both documents and if you are using the classic or namespaces package, and we'll test them using the current testing version of mergeDocx; if they use some not supported style we'll add support and send the class updated.
Regards.
p.s. we have removed the email from you username account, so it won't appear in the forum.