Hm, I don't know what it has to do with alternating substrings, but here's another version of your program :)

use strict;
use warnings;

use List::Util 'reduce';

for (1 .. 25) {
    my $digits = join '', map {int rand 2} 1 .. 100_000;
    my $substr = longest($digits);
    printf "%02d: At position (%6d), length (%6d) => $substr\n", 
        $_, index($digits, $substr), length($substr);
}

sub longest {
    return reduce {
        length($a) > length($b) ? $a : $b;
    } split /(?<=0)(?=1)|(?<=1)(?=0)/, $_[0];
}
[download]

Works a bit faster, too.