Thank you for this bug report. To properly diagnose the problem, we
need a short but complete example script to be able to reproduce
this bug ourselves. 

A proper reproducing script starts with <?php and ends with ?>,
is max. 10-20 lines long and does not require any external 
resources such as databases, etc. If the script requires a 
database to demonstrate the issue, please make sure it creates 
all necessary tables, stored procedures etc.

Please avoid embedding huge scripts into the report.

No feedback was provided for this bug for over a week, so it is
being suspended automatically. If you are able to provide the
information that was originally requested, please do so and change
the status of the bug back to "Open".

<?php
$db = new PDO('mysql:dbname=test;host=localhost', 'root', '');
$array2 = array('gb', 'us', 'nz', 'fr', 'de');
$array3 = array('fr'=>true, 'de'=>true);
$array = array_diff($array2, array_keys($array3));
reset($array);
$size = count($array);
$in = '?';
for($i = 1; $i < $size; ++$i) $in .= ', ?';
$stmt = $db->prepare('SELECT `name` FROM `table` WHERE `language` = ?
AND `code` IN('.$in.')');
$stmt->bindValue(1, 'en', PDO::PARAM_STR);
$i = 1;
$element = current($array);
do {
	$stmt->bindParam(++$i, $element, PDO::PARAM_STR);
} while(($element = next($array)) !== false);
$stmt->execute();
var_dump($stmt->fetchAll());
?>
-----------------
expected result:
array(3) {
  [0]=>
  array(2) {
    ["name"]=>
    string(4) "test"
    [0]=>
    string(4) "test"
  }
  [1]=>
  array(2) {
    ["name"]=>
    string(4) "test"
    [0]=>
    string(4) "test"
  }
  [2]=>
  array(2) {
    ["name"]=>
    string(4) "test"
    [0]=>
    string(4) "test"
  }
}
--------------------
actual result:
array(0) {
}
--------------------
db:
CREATE TABLE IF NOT EXISTS `table` (
  `name` varchar(45) NOT NULL,
  `language` enum('en','fr') NOT NULL,
  `code` char(2) NOT NULL
) ENGINE=MyISAM DEFAULT CHARSET=utf8;


INSERT INTO `table` (`name`, `language`, `code`) VALUES
('test', 'en', 'gb'),
('test', 'en', 'nz'),
('test', 'en', 'us'),
('test', 'en', 'cz');

Thank you for your bug report.

Although you supplied code to reproduce the problem, it is more complicated and longer than necessary. Please supply a short, complete and understandable piece of code to reproduce the problem. This is to make sure the problem is with PHP and not with the example.

No feedback was provided for this bug for over a week, so it is
being suspended automatically. If you are able to provide the
information that was originally requested, please do so and change
the status of the bug back to "Open".

<?php
$db = new PDO('mysql:dbname=test;host=localhost', 'root', '');
$array2 = array('fr', 'gb', 'de');
$array3 = array('de'=>true);
$array = array_diff($array2, array_keys($array3));
reset($array);
$stmt = $db->prepare('SELECT `name` FROM `table` WHERE `language` = ? AND `code` IN(?, ?)');
$stmt->bindValue(1, 'en', PDO::PARAM_STR);
$element = current($array);
$stmt->bindParam(2, $element, PDO::PARAM_STR);
$element = next($array);
$stmt->bindParam(3, $element, PDO::PARAM_STR);
$stmt->execute();
var_dump($stmt->fetchAll());
?>
---------------
actual result:
array(1) {
  [0]=>
  array(2) {
    ["name"]=>
    string(4) "test"
    [0]=>
    string(4) "test"
  }
}
---------------
expected result:
array(2) {
  [0]=>
  array(2) {
    ["name"]=>
    string(4) "test"
    [0]=>
    string(4) "test"
  }
  [1]=>
  array(2) {
    ["name"]=>
    string(4) "test"
    [0]=>
    string(4) "test"
  }
}
---------------
db:
CREATE TABLE `table` (
  `name` varchar(45) NOT NULL,
  `language` enum('en','fr') NOT NULL,
  `code` char(2) NOT NULL
);
INSERT INTO `table` (`name`, `language`, `code`) VALUES
('test', 'en', 'fr'),
('test', 'en', 'gb');
---------------
if you change

$stmt->bindParam(2, $element, PDO::PARAM_STR);
for
$stmt->bindValue(2, $element, PDO::PARAM_STR);

AND

$stmt->bindParam(3, $element, PDO::PARAM_STR);
for
$stmt->bindValue(3, $element, PDO::PARAM_STR);

you will receive expected result

i can't write it easier, so deal with it or just delete this report.

"Binds a PHP variable to a corresponding named or question mark placeholder in the SQL statement that was use to prepare the statement. Unlike PDOStatement::bindValue(), the variable is bound as a reference and will only be evaluated at the time that PDOStatement::execute() is called.", http://de2.php.net/manual/en/pdostatement.bindparam.php

At the time that you call PDOStatement::execute() you have overwritten the bound variables' value ($element) multi times. PDO does exactly what is documented: it uses the last value of $element. 

Workaround: use bindValue() instead of bindParam().