Are you sure there isn't a mistake somewhere else - maybe post some more context. When I run your example it works fine. Using CGI version 4.44

use CGI;
my $cgi = CGI->new;
my $html = $cgi->TR(
    { -height => '100', -valign => 'bottom' },
    [
        $cgi->th(['Vegetable', 'Breakfast','Lunch','Dinner']),
        $cgi->td(['Tomatoes' , 'no', 'yes', 'yes']),
    ]
);
print "$html";
[download]

OUTPUT:

<tr height="100" valign="bottom">
    <th>Vegetable</th>
    <th>Breakfast</th>
    <th>Lunch</th>
    <th>Dinner</th>
</tr>
<tr height="100" valign="bottom">
    <td>Tomatoes</td>
    <td>no</td>
    <td>yes</td>
    <td>yes</td>
</tr>
[download]