I've got the same issue: http://www.phpdocx.com/en/forum/default/topic/1172
First of all, I would like to know whether it was fixed.
Context:
I am currently using Phpdocx for merging documents.
Now, I am trying to merge a title page (one page document) with a document B containing toc, sections, lists and tables.
The second one was generated with Pandoc.
The title page document has the same style than the other one. If I generate the document B using Pandoc with the title page as template, the document B has the same content than before. "Before" means I am using another smaller .docx as template.
For merging, I use the recommended method mergeDocx from MultiMerge class.
Problem:
After merging, the bullet point lists become numbered lists.
There is something disturbing. The first bullet point list is intact but not the rest.
Experimentation:
If I merge the document B first with the title page, all bullet point lists are intact.