Short Code showing in Mail

I have a form which contains a list of checkboxes. If a box is checked, an upload field appears below the checkboxes so that the user can upload the appropriate document. Each check box has an accompanying upload field which remains hidden unless the box is checked.

The email that is sent to the form owner has an html table that shows the results. The files are at the bottom of the email, and in the html table the file name is listed next to the type of document, i.e., Final Report File Name | whatever.pdf.

In the email code, I have the group tags around the rows (tr) that display the particular field. The idea being, if the box is not click and there is no document, i.e., that particular upload field is invisible on the form, then the row is not shown in the table.

What is happening instead is that the row is there, the field in the second column is blank, and the short code is listed at the top of the email. Does that clearly paint the picture? Below you will find the form code, and the email code.

Also, here is a link to the form. It will be only for logged in users once complete, but I opened it up for you to see how it acts: https://floridaspacegrant.org/program-deliverables/

<div id="student-form" class="deliverable-form">
<div class="form-col1">
<h4 class="delivers">Program Information:</h4>
<h3>University</h3>
[select* your-university include_blank "Bethune-Cookman University" "Broward college" "Eastern Florida State College" "Eckerd College" "Embry Riddle Aeronautical University" "Florida A & M University" "Florida Atlantic University" "Florida Gulf Coast University" "Florida Institute of Technology" "Florida International University" "Florida State University" "Kennedy Space Center" "Orlando Science Center" "Space Florida" "The Astronauts Memorial Foundation" "University of Central Florida" "University of Florida" "University of Miami" "University of North Florida" "University of South Florida" "University of West Florida" "Other"]   

[group other-affiliate]
<h3>Organization Name</h3>
    [text other-organization]
[/group]

<h3>Task Order Number</h3>
    [text* order-number] 

<h3>P.I. Name</h3>
    [text* pi-name]

<h3>P.I. Phone Number</h3>
    [text* pi-number]

<h4 class="delivers">Submitter Information </h4>

<h3>Submitter's Name</h3>
    [text* submit-name]

<h3>Email</h3>
    [email* submit-email]

<h3>Contact Phone</h3>
    [text* submit-phone] 
</div>

<div class="form-col2">
<h3>Type of Deliverable:</h3>
<p style="padding:0;margin:0;margin-left:10px;">[checkbox* deliverable-options id:deliverables "Export Control Form" "China Assurance Form" "Student Longitudinal Tracking Form" "Student Awardee Questionnaire Form" "Student Authorization Form" "OEPM Report" "Final Report" "Matching Certification" "Invoice" "Other (i.e., images)" "Publications"]</p>

[group export-control-group]
<p class="upload-text">Accepted Export Control Form file types: PDF, DOC, DOCX</p>
<div>[file export-control-file limit:32mb filetypes:pdf|doc|docx]</div>
[/group]

[group china-assurance-group]
<p class="upload-text">Accepted China Assurance Form file types: PDF, DOC, DOCX</p>
<div>[file china-assurance-file limit:32mb filetypes:pdf|doc|docx]</div>
[/group]

[group student-tracking-group]
<p class="upload-text">Accepted Student Longitudinal Tracking Form file types: PDF, DOC, DOCX</p>
<div>[file student-tracking-file limit:32mb filetypes:pdf|doc|docx]</div>
[/group]

[group student-awardee-group]
<p class="upload-text">Accepted Student Awardee Questionnaire Form file types: PDF, DOC, DOCX</p>
<div>[file student-awardee-file limit:32mb filetypes:pdf|doc|docx]</div>
[/group]

[group student-authorization-group]
<p class="upload-text">Accepted Student Authorization Form file types: PDF, DOC, DOCX</p>
<div>[file student-authorization-file limit:32mb filetypes:pdf|doc|docx]</div>
[/group]

[group oepm-report-group]
<p class="upload-text">Accepted OEPM Report file types: PDF, DOC, DOCX</p>
<div>[file oepm-report-file limit:32mb filetypes:pdf|doc|docx]</div>
[/group]

[group final-report-group]
<p class="upload-text">Accepted Final Report file types: PDF, DOC, DOCX</p>
<div>[file final-report-file limit:32mb filetypes:pdf|doc|docx]</div>
[/group]

[group matching-certification-group]
<p class="upload-text">Accepted Matching Certification file types: PDF, DOC, DOCX</p>
<div>[file matching-certification-file limit:32mb filetypes:pdf|doc|docx]</div>
[/group]

[group invoice-group]
<p class="upload-text">Accepted Invoice file types: PDF, DOC, DOCX</p>
<div>[file invoice-file limit:32mb filetypes:pdf|doc|docx]</div>
[/group]

[group other-group]
<p class="upload-text">Accepted file types: PDF, DOC, DOCX, JPG, PNG</p>
<div>[file other-file limit:32mb filetypes:pdf|doc|docx|jpg|png]</div>
<div>[file other-file-two limit:32mb filetypes:pdf|doc|docx|jpg|png]</div>
<div>[file other-file-three limit:32mb filetypes:pdf|doc|docx|jpg|png]</div>
<div>[file other-file-four limit:32mb filetypes:pdf|doc|docx|jpg|png]</div>
[/group]

[group publications-group]
<p class="upload-text">Accepted Publication file types: PDF, JPG, PNG</p>
<div>[file publications-file limit:32mb filetypes:pdf|jpg|png]</div>
<div>[file publications-file-two limit:32mb filetypes:pdf|jpg|png]</div>
<div>[file publications-file-three limit:32mb filetypes:pdf|jpg|png]</div>
<div>[file publications-file-four limit:32mb filetypes:pdf|jpg|png]</div>
[/group]

<div style="margin-top:20px;">[textarea additional-info placeholder "Additional information, i.e., links to media, articles, etc"]</div>

<h6>You may e-mail additional documents to the following address: </h6>
<div><span>Dr.Jaydeep Mukherjee
FSGC Director
<a href="mailto:[email protected]">[email protected]</a>
NASA Florida Space Grant Consortium
PO Box 160650
12354 Research Parkway
Partnership 1 Building, Rom 218
Orlando  FL, 32816-0650</span></div>

</div>
<div style="clear:both;text-align:center;">
<p>[submit "Send"]</p>
</div>
</div>

<div style="border-bottom:1px dotted #999999;"><h2>Greetings, FSGC!</h2></div>

<p><strong>[submit-name]</strong> has submitted a <em>Program Deliverable</em>.  You will find all submitted information and files below.  All of this information is stored your the database and can be retrieved and exported.  You can access this data by logging in  <a href="https://www.floridaspacegrant.org/cms/login">here</a> and navigating to <em>Contact Form DB</em> in the left sidebar of your Dashboard.</p>

<table style="border-top:2px dotted #16396f;padding-top:10px;border-bottom:2px dotted #16396f;padding-bottom:10px;" cellspacing="0">

<tr height="26">
<td colspan="2" style="font-weight:bold;">Program Information</td>
</tr>

<tr height="26">
<td bgcolor="#16396f" style="padding:5px;border-bottom:1px solid #999"><strong style="padding: 5px 0 0px 10px;color:#ffffff;font-size:90%;font-family:sans-serif;">University</strong></td>
<td style="padding:5px;border-bottom:1px solid #999">[your-university]</td>
</tr>

[other-affiliate]
<tr height="26">
<td bgcolor="#16396f" style="padding:5px;border-bottom:1px solid #999"><strong style="padding: 5px 0 0px 10px;color:#ffffff;font-size:90%;font-family:sans-serif;">Other Organization</strong></td>
<td style="padding:5px;border-bottom:1px solid #999">[other-organization]</td>
</tr>
[/other-affiliate]

<tr height="26">
<td bgcolor="#16396f" style="padding:5px;border-bottom:1px solid #999"><strong style="padding: 5px 0 0px 10px;color:#ffffff;font-size:90%;font-family:sans-serif;">Task Order Number</strong></td>
<td style="padding:5px;border-bottom:1px solid #999">[order-number]</td>
</tr>

<tr height="26">
<td bgcolor="#16396f" style="padding:5px;border-bottom:1px solid #999"><strong style="padding: 5px 0 0px 10px;color:#ffffff;font-size:90%;font-family:sans-serif;">PI Name</strong></td>
<td style="padding:5px;border-bottom:1px solid #999">[pi-name]</td>
</tr>

<tr height="26">
<td bgcolor="#16396f" style="padding:5px;border-bottom:1px solid #999"><strong style="padding: 5px 0 0px 10px;color:#ffffff;font-size:90%;font-family:sans-serif;">PI Phone Number]</strong></td>
<td style="padding:5px;border-bottom:1px solid #999">[pi-number]</td>
</tr>

<tr height="26">
<td colspan="2" style="font-weight:bold;">Submitter Information</td>
</tr>

<tr height="26">
<td bgcolor="#16396f" style="padding:5px;border-bottom:1px solid #999"><strong style="padding: 5px 0 0px 10px;color:#ffffff;font-size:90%;font-family:sans-serif;">Name</strong></td>
<td style="padding:5px;border-bottom:1px solid #999">[submit-name]</td>
</tr>

<tr height="26">
<td bgcolor="#16396f" style="padding:5px;border-bottom:1px solid #999"><strong style="padding: 5px 0 0px 10px;color:#ffffff;font-size:90%;font-family:sans-serif;">Email</strong></td>
<td style="padding:5px;border-bottom:1px solid #999">[submit-email]</td>
</tr>

<tr height="26">
<td bgcolor="#16396f" style="padding:5px;border-bottom:1px solid #999"><strong style="padding: 5px 0 0px 10px;color:#ffffff;font-size:90%;font-family:sans-serif;">Phone Number</strong></td>
<td style="padding:5px;border-bottom:1px solid #999">[submit-phone]</td>
</tr>

<tr height="26">
<td colspan="2" style="font-weight:bold;">Type of Deliverable</td>
</tr>

<tr height="26">
<td colspan="2">[deliverable-options]</td>
</tr>

[export-control-group]
<tr height="26">
<td bgcolor="#16396f" style="padding:5px;border-bottom:1px solid #999"><strong style="padding: 5px 0 0px 10px;color:#ffffff;font-size:90%;font-family:sans-serif;">Export Control File Name</strong></td>
<td style="padding:5px;border-bottom:1px solid #999">[export-control-file]</td>
</tr>
[/export-control-group]

[china-assurance-group]
<tr height="26">
<td bgcolor="#16396f" style="padding:5px;border-bottom:1px solid #999"><strong style="padding: 5px 0 0px 10px;color:#ffffff;font-size:90%;font-family:sans-serif;">China Assurance File Name</strong></td>
<td style="padding:5px;border-bottom:1px solid #999">[china-assurance-file]</td>
</tr>
[/china-assurance-group]

[student-tracking-group]
<tr height="26">
<td bgcolor="#16396f" style="padding:5px;border-bottom:1px solid #999"><strong style="padding: 5px 0 0px 10px;color:#ffffff;font-size:90%;font-family:sans-serif;">Student Longitudinal Tracking File Name</strong></td>
<td style="padding:5px;border-bottom:1px solid #999">[student-tracking-file]</td>
</tr>
[/student-tracking-group]

[student-awardee-group]
<tr height="26">
<td bgcolor="#16396f" style="padding:5px;border-bottom:1px solid #999"><strong style="padding: 5px 0 0px 10px;color:#ffffff;font-size:90%;font-family:sans-serif;">Student Awardee Questionnaire File Name</strong></td>
<td style="padding:5px;border-bottom:1px solid #999">[student-awardee-file]</td>
</tr>
[/student-awardee-group]

[student-authorization-group]
<tr height="26">
<td bgcolor="#16396f" style="padding:5px;border-bottom:1px solid #999"><strong style="padding: 5px 0 0px 10px;color:#ffffff;font-size:90%;font-family:sans-serif;">Student Authorization File Name</strong></td>
<td style="padding:5px;border-bottom:1px solid #999">[student-authorization-file]</td>
</tr>
[/student-authorization-group]

[oepm-report-group]
<tr height="26">
<td bgcolor="#16396f" style="padding:5px;border-bottom:1px solid #999"><strong style="padding: 5px 0 0px 10px;color:#ffffff;font-size:90%;font-family:sans-serif;">OEPM Report File Name</strong></td>
<td style="padding:5px;border-bottom:1px solid #999">[oepm-report-file]</td>
</tr>
[/oepm-report-group]

[final-report-group]
<tr height="26">
<td bgcolor="#16396f" style="padding:5px;border-bottom:1px solid #999"><strong style="padding: 5px 0 0px 10px;color:#ffffff;font-size:90%;font-family:sans-serif;">Final Report File Name</strong></td>
<td style="padding:5px;border-bottom:1px solid #999">[final-report-file]</td>
</tr>
[/final-report-group]

[matching-certification-group]
<tr height="26">
<td bgcolor="#16396f" style="padding:5px;border-bottom:1px solid #999"><strong style="padding: 5px 0 0px 10px;color:#ffffff;font-size:90%;font-family:sans-serif;">Matching Certification File Name</strong></td>
<td style="padding:5px;border-bottom:1px solid #999">[matching-certification-file]</td>
</tr>
[/matching-certification-group]

[invoice-group]
<tr height="26">
<td bgcolor="#16396f" style="padding:5px;border-bottom:1px solid #999"><strong style="padding: 5px 0 0px 10px;color:#ffffff;font-size:90%;font-family:sans-serif;">Matching Certification File Name</strong></td>
<td style="padding:5px;border-bottom:1px solid #999">[invoice-file]</td>
</tr>
[/invoice-group]

[other-group]
<tr height="26">
<td bgcolor="#16396f" style="padding:5px;border-bottom:1px solid #999"><strong style="padding: 5px 0 0px 10px;color:#ffffff;font-size:90%;font-family:sans-serif;">Other File Name</strong></td>
<td style="padding:5px;border-bottom:1px solid #999">[other-file] [other-file-two] [other-file-three] [other-file-four]</td>
</tr>
[/other-group]

[publications-group]
<tr height="26">
<td bgcolor="#16396f" style="padding:5px;border-bottom:1px solid #999"><strong style="padding: 5px 0 0px 10px;color:#ffffff;font-size:90%;font-family:sans-serif;">Publications File Name</strong></td>
<td style="padding:5px;border-bottom:1px solid #999">[publications-file] [publications-file-two] [publications-file-three] [publications-file-four]</td>
</tr>
[/publications-group]

<tr height="26">
<td bgcolor="#16396f" style="padding:5px;border-bottom:1px solid #999"><strong style="padding: 5px 0 0px 10px;color:#ffffff;font-size:90%;font-family:sans-serif;">Additional Information</strong></td>
<td style="padding:5px;border-bottom:1px solid #999">[additional-info]</td>
</tr>

</table>

When I receive the email, it comes through like this (screenshot): https://floridaspacegrant.org/email-screenshot.png

I would prefer that the rows without data not show up, and of course, the shortcode at the top is the real problem.