It's apparently an auto-vivification problem, caused by iterating over the entire structure? Using the following subroutine instead of the grep produces the same results:

dump_matrix();

sub dump_matrix {
   for my $i (0..2) {
       print "row: $i [ ";
       for my $j (0..3) {
           print "$matrix[$i][$j], ";
       }
       print "]\n";
   }
}
[download]

What's interesting is how two consecutive calls to Data::Dumper without intervening code does not reproduce the anomaly (even if you pass by reference). Makes me wonder how Data::Dumper is traversing the structure.

--Jim

Update: Ah. Thanks tachyon, I would've researched it but I've been competing for computer time today. Five year olds always win :(