michael@zaphod:~>php
<?
$a = array(array(1, "a"), array(2, "b"), array(3, "c"));
$b = array(array(1, "a"), array(2, "b"), array(4, "d"));
$c = array_intersect($a, $b);

var_dump($c);
?>
X-Powered-By: PHP/4.0.6
Content-type: text/html

array(3) {
  [0]=>
  array(2) {
    [0]=>
    int(1)
    [1]=>
    string(1) "a"
  }
  [1]=>
  array(2) {
    [0]=>
    int(2)
    [1]=>
    string(1) "b"
  }
  [2]=>
  array(2) {
    [0]=>
    int(3)
    [1]=>
    string(1) "c"
  }
}

The same thing happens in 4.0.5.

For comparison 4.0.4pl1-Output (and as I expect it to be):

X-Powered-By: PHP/4.0.4pl1
Content-type: text/html

array(2) {
  [0]=>
  array(2) {
    [0]=>
    int(1)
    [1]=>
    string(1) "a"
  }
  [1]=>
  array(2) {
    [0]=>
    int(2)
    [1]=>
    string(1) "b"
  }
}