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.

Sorry, a script that creates databases and such and also reproduces the bug in 
under 20 lines of code? That's impossible.

Well, than it's impossible to help you, and I have to assume the bug is in your code.

php -r '$p1=new PDO("mysql:dbname=test"); $p2=new PDO("mysql:dbname=test"); $p1->exec("drop table if exists t1"); $p1->exec("create table t1 (id int auto_increment primary key)"); foreach (array($p1,$p2) as $p) $p->exec("insert into t1(id) values(NULL)"); foreach (array($p1,$p2) as $p) var_dump($p->query("SELECT LAST_INSERT_ID()")->fetchAll());'

array(1) {
  [0]=>
  array(2) {
    ["LAST_INSERT_ID()"]=>
    string(1) "1"
    [0]=>
    string(1) "1"
  }
}
array(1) {
  [0]=>
  array(2) {
    ["LAST_INSERT_ID()"]=>
    string(1) "2"
    [0]=>
    string(1) "2"
  }
}

php -r '$p1=new PDO("mysql:dbname=test",null,null,array(PDO::ATTR_PERSISTENT=>1)); $p2=new PDO("mysql:dbname=test",null,null,array(PDO::ATTR_PERSISTENT=>1)); $p1->exec("drop table if exists t1"); $p1->exec("create table t1 (id int auto_increment primary key)"); foreach (array($p1,$p2) as $p) $p->exec("insert into t1(id) values(NULL)"); foreach (array($p1,$p2) as $p) var_dump($p->query("SELECT LAST_INSERT_ID()")->fetchAll());'
array(1) {
  [0]=>
  array(2) {
    ["LAST_INSERT_ID()"]=>
    string(1) "2"
    [0]=>
    string(1) "2"
  }
}
array(1) {
  [0]=>
  array(2) {
    ["LAST_INSERT_ID()"]=>
    string(1) "2"
    [0]=>
    string(1) "2"
  }
}