In mysql/bin/my.ini you still configure innodb_additional_mem_pool_size=2M.
In old versions of MySQL, the default was 1M, so that this setting in fact raised the amount of available space. In MySQL 5.6 however, the default already is 8M. So basically you are no longer raising, but you are now reducing it. This is not, what was intended. Additionally this setting is deprecated and scheduled for removal from the MySQL core.
I would recommend removing this setting from configuration.