Hi,
I suppose the issue is a logic issue.
If you configure the user points to be added as a virtual coupon ( it's the case by default), the points payment is added directly to the cart as a negative fee corresponding to the total amount. However, the payment fee is calculated after that, and since the total amount is 0, 5% of 0 is still 0 and thus no payment fee is added.
Could you provide a screenshot of all the settings of your _user points payment method so that we can get a better idea of the situation to reproduce it on our end ?