'Payment Methods' is blank on the emailed PDF but not on the manually created PDF

Unfortunately Magento only provides pdf templates in the admin context. If you are using the attach pdf to order email this email is sent in the frontend context resulting in an empty payment method block in the pdf.

The easiest solution is to copy the templates from app/design/adminhtml/default/default/template/payment/info/pdf to app/design/frontend/base/default/template/payment/info/pdf

If your payment method comes with its own pdf template files these would need to be copied in a similar fashion.