This is a PHP list
Exactly. And it is the switch from --with-mysql=/usr to --with-mysql=mysqlnd (the PHP native MySQL driver) during the build that caused the problem. And there is no alternative to building current PHP versions with mysql support than with mysqlnd, because the mysql 5.5.x libraries don't work against PHP 5.2 and PHP 5.3, although they are out for months.
but most likely run: mysql_fix_privilege_tables and then restart mysql.
As I said: The problem is not at the MySQL server, it must be at the client side.
Kind regards
Marten