After migrating to version 6.0, check the central audit log for messages indicating a problem. In particular, check for Directory Server users whose password changes may have been missed during the migration process. Such errors would be similar to the following:
[16/Apr/2004:14:23:41.029 -0500] WARNING 14 CNN101 ds-connector-host.example.com "Unable to obtain password of user cn=JohnSmith,ou=people,dc=example,dc=com, because the password was encoded by a previous installation of Identity Synchronization for Windows Directory Server Plugin. The password of this user cannot be synchronized at this time. Update the password of this user again in the Directory Server."
You will not see this log message until after you start synchronization in Identity Synchronization for Windows 6.0. This is why checking the logs is the last step of the migration procedure.