Testing your files on my server, the address 1 and address 2 information is being sent in the email properly.
make sure your updates are being uploaded to the server correctly.
I still see some bad element names in your form:
<input name="Master_Certificate_Program?" type="checkbox" id="MastersCertification" value="Yes">
your form element names may only contain letters and numbers. The only exception is the underscore character.