njahnke,

You may know this already, so it may not actually help your situation, but if you execute this untested code:

  my @array;
  $array[0] = "stuff";
  $array[10_000] = "more-stuff";
  print scalar( @array ),"\n";
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The result is 10,001 which is 2 defined array elements and 9,999 undefined elements. If the above variable was a hash you would have 2 defined and existing elements.

Are you sure your not created large gaps in your arrays that seem to be 'leaking'?

Good Luck!