Hi,
1. If you confirm manually an order from the backend orders listing, is the user group attached to the customer's user account ?: NO
Like Nicolas wrote, you need to check your plugin configuration and HikaShop configuration.
Modifying the order status directly in the backend should trigger the plugin which should modify the user group.
So, before start a deeper investigation, we need to be sure that your HikaShop configuration is good.
So please indicate the setting "Payment confirmed order status", the content of the order and the status of the order.
The plugin will only be triggered when the order will receive the "Payment confirmed order status" status and only that one.
It could be also interesting to know if the product is a product with characteristics or not ; because the plugin check only the bought product and not his parent (if it's a variant).
Regards,