When you come across problems like these it is a good idea to add some print statements to your script to see what is going on. So if you added some lines like this:

if ($query->param('submit1')){
    my $family = $query->param('family');
    my $TB = $query->param('TB');
    my $LM = $query->param('LM');
    my $HS = $query->param('HS');
    my $SC = $query->param('SC');
    my $AT = $query->param('AT');
    print qq|TB: $TB<br>|;
    print qq|LM: $LM<br>|;
    print qq|HS: $HS<br>|;
    print qq|SC: $SC<br>|;
    print qq|AT: $AT<br>|;
[download]

You would see that if any of the checkboxes were ticked they have the value 'on' which is probably not what you want. So the problem is with your HTML - you could change the 'value' attribute of the checkbox to:

<input type="checkbox" name="TB" value="TB">Trypanosoma brucei<br>
<input type="checkbox" name="LM" value="LM">Leishmania major<br>
<input type="checkbox" name="HS" value="HS">Homo sapiens<br>
<input type="checkbox" name="SC" value="SC">Saccharomyces cerevisiae<b
+r>
<input type="checkbox" name="AT" value="AT">Arabidopsis thaliana<br>
[download]

It is also a good idea to check the values from your form before passing the query to the database