Hello,
Does your DOCX contain the custom styles you want to use? To include custom styles in a DOCX with MS Word is not enough to generate an empty DOCX. Contents with the needed styles must be added, otherwise MS Word won't include them in the DOCX.
For futher support, please send the custom_template.docx file you are using to contact[at]phpdocx.com and we'll check it.
Regards.