The first thing to check when areas of a custom email template are not displayed is the Display Conditions for both the text box and the section. Both text boxes and sections have individual Display Conditions. This is to increase flexibility and customization.

Sections are highlighted red when selected and can contain multiple text boxes and content items. When a section is selected, the Section editor will appear on the right side. Within this editor, you will see Display Conditions. Adjust the display conditions as necessary for your desired results.

Text boxes and content items highlight blue when selected. Each individual text box has it's own display conditions. Select the section that is not displaying on the final product and adjust the display conditions as necessary for your desired results.

For more information: 4. Variables and Display Conditions | TimeZest Help Center