Hello,
With the same general settings "Manual by Member", we have tested it and cannot reproduce the similar issue. The result is that the new member is placed under the correct sponsor (although the plan is not the same) and the commission is also generated for the sponsor.
Here is how we reproduce the registration process:
1- Visit the sponsor's referral URL, on the registration page the sponsor's username is displayed correctly
2- Fill out the registration form
3- Login to the member area, in the dashboard all available plans are displayed
4- Select the plan to register, confirm the sponsor is the same, process the payment
5- New member is activated, and commissions are generated for the sponsor
If the issue is still exist in your part, please provide the video of it, we will have a look at it.
Regards,