Perl provides the C, isprint() function as isPRINT() which tests whether or not a character is printable. http://perldoc.perl.org/perlclib.html#Character-Class-Tests. I would consider using that to filter out these unprintable characters that seem to be messing up the comparison.

Perhaps using regex:

#!/usr/bin/perl -w
use strict;

my $version_on_disk = "\aabfd\nadsf\n\n555";
my $version_dns ="lkjh\a\n\r\n\a89";

foreach ($version_on_disk, $version_dns)
{
   $_ =~ s/[^[:print:]]//g; #delete non-printable chars
}

print "$version_on_disk $version_dns\n";
#prints: abfdadsf555 lkjh89
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