Consider:

use strict;
use warnings;
use 5.012;
use Data::Dumper;

my $s1 = '45 20 00 00 00 03 00';
my $s2 = '40 20 00 00 00 00 00';

while ((my @a = $s1 =~ /(\d{2})/g) && (my @b = $s2 =~ /(\d{2})/g)){
    say "found $a[0] and $b[0] !!!";
    say Dumper(\@a, \@b);
}
[download]

A regex in list context will give you all matches at once.

Next time the loop comes around, it starts all over again as it has exhausted its matching and resets.

This code will do what you want:

use strict;
use warnings;
use 5.012;
use Data::Dumper;

use List::MoreUtils qw/each_array/;

my $s1 = '45 20 00 00 00 03 00';
my $s2 = '40 20 00 00 00 00 00';

my @first  = $s1 =~ /(\d{2})/g;
my @second = $s2 =~ /(\d{2})/g;
my $ea = each_array(@first, @second);

while (my ($first, $second) = $ea->()){
    say "found $first and $second !!!";
}
[download]