PHP doesn't use the Windows certificate infrastructure, as it uses OpenLDAP libraries (unless you compile it yourself to use another supported LDAP library like Oracle's or Novell's). So it won't look for your CA certificate in the trusted root certificates store (or any of the other stores).
You need to convert our CA certificate to a PKCS#12 certificate in PEM format. You can do that by exporting the CA certificate from the store into "Base64-encoded x509 (.CER)" format.
Once you have your CA certificate you can follow the instructions at http://www.php.net/manual/en/function.ldap-start-tls.php#94815 You just need steps 2-4 (and the name of the CA certificate file can be whatever you want).
That should set you going. The instructions from the link only verify that the LDAP server certificate is signed by the CA certificate, but doesn't verify the certificate itself. If you want to do that, you need additional configuration.
Saludos. Iñaki.