I've taken a few shortcuts for you, and added a check to be sure you don't get more than one occurrence of any number in a line.

$| = 1;

print qq(
-------------------------------------------------------
National Lottery Number Picker
-------------------------------------------------------
How many lines do you want to play?  );

my $num_lines = <STDIN>;
$num_lines =~ s/\D+//g;
die "Good.  Don't waste your money!\n" unless $num_lines;

my @numbers = (1..49);
my $output;

for (1..$num_lines) {
    my @line = ();
    my %chosen = ();
    for (1..6) {
        my $element;
        while (!$element || $chosen{$element}) {
            $element = $numbers[rand @numbers];
        }
        push @line, $element;
        $chosen{$element} = 1;
    }
    $output .= join "\t", sort {$a <=> $b} @line;
    $output .= "\n";
}

print $output;

# Then, do your e-mail thing.  Send $output as the message
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