Just a supplement to the advice given by Anonymous Monk:

Data::Dumper provides a Useqq configuration variable which, when set, causes Dumper to print any newline, tab, or carriage return characters as \n, \t, and \r, respectively. This makes it easier to see exactly what is present in each variable. Here is how I would deploy this feature to begin the debugging process:

...
use Data::Dumper;
$Data::Dumper::Indent = 0;
$Data::Dumper::Terse  = 1;
$Data::Dumper::Useqq  = 1;
...
foreach my $key (sort keys %ref) {
    ...
    foreach(@temp) {
        if ($temp[0] == 2) {
            printf "\$key = %s\n  \$ref{%s} = %s\n  \$probes[%s] = %s\
+n",
                    Dumper($key),
                    Dumper($key), Dumper($ref{$key}),
                    Dumper($key), Dumper($probes[$key]);
            print $key."\t".$ref{$key}."\t".$probes[$key];
        }
    }
}
[download]

Hope that helps,