PRO email templates can use any of the following merge fields, whereas company signatures can only use the Company and User fields:
If you're going to use any of the "User" merge fields (ex User Name), please ensure that either your global company email signature doesn't contain this information, or you've deselected the "Use Default Signature" checkbox when creating the email template.
Please ensure that data exists in the Project for any merge field you're using in your email template. You can preview your email before sending it to verify that it is formatted correctly.
If you'd like to learn how to use these merge fields or where the data is pulling for a certain merge field, click here.