Hi,
If it works when you manually change the status in the backend and that it doesn't when the status is changed automatically by a third party payment plugin, it feels more related to that payment plugin than HikaShop.
Check if you see the email in the Email history of HikaShop.
Also, you could test with PayPal and a sandbox account to see if you get the email when the PayPal payment notification changes the order status to confirmed.
As a matter of fact, we've have many (hundreds if not thousands) of merchants already updating to HikaShop 2.6.4 and no one yet reported a problem with HikaShop not sending order status notifications to customers.
This is a critical piece of an online shop and would have been notified to us several times one or two days after the release.
So I highly doubt that the problem is in HikaShop (and of course, if I do a test with a PayPal payment on our end with the 2.6.4, it works).
Maybe you need to update your payment plugin ? And maybe you want to contact the support of that payment plugin. They might be able to help on that end too.