The custom email template has a fixed structure and it is not adjusted to new changes, as the Default Template. When you create a custom template it pertains to that selected form. Field IDs in the template are mapped. A new form has different field IDs and that is why you are receiving wrong form content if you you are not matching the correct email template with the correct form.
The most probable cause for this is the fact that you’ve got several templates in your Email Templates section and that they are not associated correctly with your forms.
When you access the Email Templates section, you see all the templates that you’ve got in your account, for all the forms (so not just the templates pertaining to the one form that you are tweaking at that moment).
In order to avoid any issues, make sure to give suggestive names to your email templates and to use them for the right forms.
CaptainForm recommends naming the email template after the form’s title. This is the best way to keep track of email templates.