CGI and Perl will let you easily label your checkboxes. See the following (untested) sample:

my @values;
my %labels;

foreach(1..10)
{
  $values[$_] = $_;
  $labels{$_} = "Item $_";
}

$colgroup = $cgi->checkbox_group(
                    -name=>'embl_group',
                    -values=>\@values,
                    -labels=>\%labels,
                    -linebreak=>'true'
                  );
[download]

This will let you have your item names and checkboxes that correspond with them in the same cell of the table. This should take care of your alignment problem.

Hope this helps!
MrCromeDome