Received a notification and payment for one incomplete payment and none for other. Why is there a difference?

One of the "incomplete payments" submissions I did in fact get an email notification about and can see the money.

Another one I haven't received anything. Why is there a difference?

The incomplete submissions cannot process any payments and the email alerts are triggered only when Pending Payment Emails option is enabled from the Payment field properties. The submission that you've received the payment could be another submission from the same user.

Since you have not set the Pending Payment Email on your JotForm, the emails are not triggered and the payment is not processed for the other submission. You should be able to see such submissions from Incomplete Payments.

Hope this information helps!