Hello,
We'd need to check the PEM file. Maybe the PEM file you are using doesn't include all needed information or you need to use SignPDFPlus added with the release of phpdocx 12:
https://www.phpdocx.com/news/post/phpdocx-v12-release-notes/223
https://www.phpdocx.com/api-documentation/digital-signature-package/digitally-sign-docx-pdf-with-PHP
If you send a sample PEM to contact[at]phpdocx.com we'll do some tests.
Regards.