Why doesn't the notification email show both uploads?

When we asked people to upload all requested files in one upload field, they were forgetting to upload all files. So I separated the questions and ask visitors to upload for each question.

The problem is that only one upload appears in the email. Is there something special to do to get both uploads to display in the email?

I have inspected your email Notification settings and I saw that some fields and values of those fields are missing inside of your Email Notification settings and that is the reason why you are not getting all data inside of email submissions. Only value of second upload field is shown inside of your email Notification and value of your first upload field is missing. You need to add value of first upload field to your email Notification as well.  

I would suggest you to create new Email Notification and delete old one. When you create new Notification all fields and values of fields will be automatically added inside of your Email Notification.

Hope this will help. Let us know if you need further assistance.