@a puts $s1 =~ /(\d{2})/g in list context so all matches will be found and used to populate @a. You probably want something like:

#!/usr/bin/perl
use warnings;
use strict;

my $s1 = "45 20 00 00 00 03 00";
my $s2 = "40 20 00 00 00 00 00";
my @a1 = $s1 =~ /(\d{2})/g;
my @a2 = $s2 =~ /(\d{2})/g;

die "Mismatched lists" if @a1 != @a2;
print "found $a1[$_] and $a2[$_]\n" for 0 .. $#a1;
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Prints:

found 45 and 40
found 20 and 20
found 00 and 00
found 00 and 00
found 00 and 00
found 03 and 00
found 00 and 00
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