Hi,
The HikaShop point does not have the features of the AlphaUserPoints one ?
I am really surprised because, the User point plugins have more features than the AUP one.
About your problem, you should list all valid statuses which allow the user to have his points.
Your configuration just have "confirmed", so if the order status is not "confirmed", the customer should not have his points, so the plugin will remove his points.
You have to also include "shipped" in the list of the statuses. Otherwise "shipped" will be consider as the same as "cancelled", for example.
Regards,