Not sure what's going wrong for you but this script

use strict;
use warnings;
use Spreadsheet::WriteExcel;

my $file = "test.xls";
my $xWB = Spreadsheet::WriteExcel->new($file);
my $xWS5 = $xWB->add_worksheet('Summary');

my $format = $xWB->add_format();
$format->set_bold();

my $row_count = 5;
my $multiply = $xWS5->store_formula("=E2*F2");

for my $line (0..$row_count) {
    $xWS5->repeat_formula($line, 6, $multiply, $format, "E2", 'E'.($li
+ne + 1), "F2", 'F'.($line + 1));
}
[download]

creates a new spreadsheet 'test.xls' with a 'Summary' tab and formulae

=E1*F1
=E2*F2
=E3*F3
=E4*F4
=E5*F5
=E6*F6
[download]

in cells G1 to G6, which I understand is what you want.

As an additional remark I would think that the for my $line ... loop should not be with the while (my $ar = ... loop, as it repeats the same operation each time. This should not make a difference but is rather wasteful.