You may find that a payment does not appear due to restrictions on your Sphere login.  If your login is limited to a specific Virtual Account, you will not be able to see payments made to a Virtual Account that you do not have access to see.

There is another case where Virtual Accounts can impact your ability to view a payment.  If a payment is made directly to a contact record and is restricted to a Virtual Account, you will not be able to see it in the Payment Details Report so long as you have a Virtual Account restriction on your login.  Note, this only applies to transactions applied directly to a contact record.  Event-based transactions will appear appropriately.

If you access the Payment Details Report as an administrator user in the Sphere account, you will be able to see all payments regardless of where they are logged in Sphere.

If you would like clarification on this or find that your issue does not match the above explanation, chat With Support and reference this article.