The problem is in this block of code in application/helpers/export_helper.php. The -- if ($i<$num_fields && !$field['hide']) -- should apply to the --echo-- of the field, not just the delimiter:

// Add column headers (used by R export)
if($header==TRUE)
{
    $i = 1;
    foreach ($fields as $field) {
        echo $q.strtoupper($field['sql_name']).$q;
        if ($i<$num_fields && !$field['hide']) echo ',';
        $i++;
    }
    echo("\n");