I'm not clear about your question -- where are things getting added to the flat data file? And what do you mean by "sent to the next line"?

That said, here's a cleanup of the code you posted:

open FILE, "$catdir/categories.dat" or
    error_message( "Can't find data file: $catdir/categories.dat" );
@list = <FILE>;
close FILE;

chomp @list; #remove newlines

print "<select size=\"1\" name=\"catlisting\>\n";
foreach my $element ( sort @list ) {
    print "<option value=\"$element\">$element</option>\n";
}
print "</select>";
[download]

I replaced the loop with a more natural foreach loop, removed the duplicate "close" statement, and removed the mystery split statement ( which does nothing, based on your data file provided ).