Please try using this CVS snapshot:

  http://snaps.php.net/php5.2-latest.tar.gz
 
For Windows (zip):
 
  http://snaps.php.net/win32/php5.2-win32-latest.zip

For Windows (installer):

  http://snaps.php.net/win32/php5.2-win32-installer-latest.msi

I have setting up the cvs version and the problem occurs again.

And you really updated ALL dlls using the ones from the snapshot package?

Yes i have copied the .dll/.exe/.lib from the .zip to my C:\Program Files\PHP directory.
Then restart IIS and the problem occurs again.

More informations :
- The problem occurs since the php installation with the installation package. So i have the problem from the beggining i start using php with IIS.
- My customers php files is on a Samba Server and PHP is installed on 2 HTTP servers (load balancing answer) and the problem occurs for both.
- I have no problem with ODBC MySQL connector (fast connection) and ASP run fast on these servers.
- I have set to "on" the "output_buffering" option. I have see it could solve my problem but no finally.
- I have "C:\Program Files\PHP" in my PATH variable.

I think the progress of the execution of this script is like this:
1/ File is loaded from the samba server. Everything is OK.
2/ Php is launched and start interpreting it. Everything is OK.
3/ Php needs to use MySQL ! The slowdown occurs here. Maybe problem to locate phpmysql.dll or anything else.
4/ Php contacts MySQL Server and sends requests. Eveything is OK.
5/ Php prints result to the browser.

How exactly are you connecting to Mysql? Exactly _what_ line is used? Do you connect using the IP of the mysql server?

I have tested with the fqdn and with the IP address, result is the same.
I have added the fqdn in my host file in windows and result is the same.
It's big application like phpbb or joomla who get this problem ... So i think they use mysql_connect(). I haven't tested small scripts on the servers.

Try the smallest possible script. Just "mysql_connect()" with proper parameters..

I have make a very small script and the connection, execution is fast.
Everything is fine. Very strange.

Here the small script:
$db_link = mysql_connect("xxxxx", "user", "pass");
mysql_select_db("database");
$ret = mysql_query("SELECT * FROM zp_options");
while ($tmp = mysql_fetch_array($ret))
  print_r($tmp);
mysql_close($db_link);

Then you need to figure out what really is the bottleneck. It doesn't seem to be mysql_connect(), so check the phpbb/joomla/whatever you're experiencing with, what they're actually using to connnect to mysql. I'd use something like Xdebug to figure out where the real problem is..

I have seting-up the xdebug module on 1 of our production server.
I got a big backtrace for the script and i take 16 seconds to get executed.

Finally I have see that some operation on files take severals times, like file_exists(), example:
   3.2642    1477720               -> file_exists('\\\\192.168.0.1\\windows\\website\\ssp_director\\app\\vendors\\cache_engines/file.php') \\192.168.0.1\windows\website\ssp_director\app\cake\basics.php:621
                                     >=> FALSE
    3.4922    1477840               -> file_exists('\\\\192.168.0.1\\windows\\website\\ssp_director\\app\\vendors\\cache_engines/file.php') \\192.168.0.1\windows\website\ssp_director\app\cake\basics.php:623

So this function take 228ms to execute, and the file_exists is executed 30 times so 7 seconds only for this function.
Every access to the files on the server seems to be quite slow. Does php for windows use a special lock system who is slow on the samba server?

No, this is just inherent behaviour and nothing to do with PHP.