Ah, got it. I've modified the call to:

  NestedLoops(
    [ 
      ( sub {
        my $prefix = join '', @x[@_];
        [ grep !$seen{$prefix . $x[$_]}++, ($_ ? $_ + 1 : @_) .. $#x ]
+;
      } ) x $n,
    ],
    sub {
      my $ssx = join '', @x[@_];
      $count += (matchss($ssx, $y) or return) * matchss($ssx, $x);
    },
  );
[download]

.. and that's working fine; a dump of %seen confirms that it is seeing only genuine repeats.

Of course, now that I've unified the loop specifier, it feels slightly wasteful having to create $n copies of the same subref, but I can live with that. :)

Thanks for the help.

Hugo