I have simplified the reproduce code to much. Sorry

it should be

$iterator = new RecursiveIteratorIterator(new RecursiveArrayIterator($arr['l1']));
foreach($iterator as $leaf) {
    $iterator->offSetSet($iterator->key(), 'ALTER' );
}

Expected result
array(3) refcount(2){
  ["l1"]=>
  array(1) refcount(1){
    ["one"]=>
    array(1) refcount(1){
      ["two"]=>
      string(5) "ALTER" refcount(1)
    }
  }
  ["l2"]=>
  array(1) refcount(1){
    ["one"]=>
    array(1) refcount(1){
      ["two"]=>
      string(3) "ORG" refcount(2)
    }
  }
  ["l3"]=>
  array(1) refcount(1){
    ["one"]=>
    array(1) refcount(1){
      ["two"]=>
      string(3) "ORG" refcount(1)
    }
  }
}

Actual Result 
array(3) refcount(2){
  ["l1"]=>
  array(1) refcount(3){
    ["one"]=>
    array(1) refcount(1){
      ["two"]=>
      string(5) "ALTER" refcount(1)
    }
  }
  ["l2"]=>
  array(1) refcount(1){
    ["one"]=>
    array(1) refcount(1){
      ["two"]=>
      string(3) "ORG" refcount(2)
    }
  }
  ["l3"]=>
  array(1) refcount(3){
    ["one"]=>
    array(1) refcount(1){
      ["two"]=>
      string(5) "ALTER" refcount(1)
    }
  }
}

What if you didn't pay attention to the internals like refcount but only for actual results? Can you come up with a short and simple example of what actually doesn't work?

Create a ArrayIterator on branch1. Alter the leaf by using iterator. Leave on branch2 are affected too.

Simplified reproduce code.

$data['one'] = 'ORG';
$arr = array (
	'branch1' => $data,
	'branch2' => $data,
);
$iterator = new ArrayIterator($arr['branch1']);;
$iterator->offSetSet($iterator->key(), 'ALTER' );
var_dump($arr);

Expected result
array
  'branch1' => 
    array
      'one' => string 'ALTER' (length=5)
  'branch2' => 
    array
      'one' => string 'ORG' (length=3)


Actual result
array
  'branch1' => 
    array
      'one' => string 'ALTER' (length=5)
  'branch2' => 
    array
      'one' => string 'ALTER' (length=5)

Since the iterator does not modify original array, this is the expected result of your script (and what I get using latest CVS build):

array(2) {
  ["branch1"]=>
  array(1) {
    ["one"]=>
    string(3) "ORG"
  }
  ["branch2"]=>
  array(1) {
    ["one"]=>
    string(3) "ORG"
  }
}

I did my test on 5.2.3 release on window and solaris.
I don't understand why you say original array is not modified since i'm using offsetSet function, it should modified $arr and it does.

If i init $arr with $data1 and $data2 like this, only branch one is altered.

$data1['one'] = 'ORG';
$data2['one'] = 'ORG';
$arr = array (
	'branch1' => $data1,
	'branch2' => $data2,
);

But I'm using latest CVS. Perhaps you should have tried it too before reporting already fixed bug.

I can't access to cvs or svn through my company's firewall.
I see  there is a zip with snaps for windows but the download server is currently offline for maintenance.

Anyway, with the result you gave me, 'ORG' on both branch, the problem is not solve for me. ArrayIterator should be able to modify the array. And at least, it has always been able too until now.

I finally download snap.
This snapshot was automatically generated on
Fri, 17 Aug 2007 00:08:51 -0400

Version: 5.2.4RC3-dev
Branch: HEAD
Build: Release_TS

The bug is still there. Take a look to the added dump of $data. $data is altered to. This can't be the expected result. $data is never used as reference.

Reproduce code
$data[] = 'ORG';
$arr1 = array ('branch1' => $data, 'branch2' => $data);

$iterator = new ArrayIterator($arr1['branch1']);;
$iterator->offSetSet($iterator->key(), 'ALTER' );

var_dump($arr1);
var_dump($data);

Actual result.
array(2) {
  ["branch1"]=>
  array(1) {
    [0]=>
    string(5) "ALTER"
  }
  ["branch2"]=>
  array(1) {
    [0]=>
    string(5) "ALTER"
  }
}
array(1) {
  [0]=>
  string(5) "ALTER"
}