Child account invoices don't populate under parent when receiving payment

Hi all!  We have several customers that have a lot of child accounts (some have over a 1,000 child accounts).  All of the child accounts are nested under the parent and the checkbox is checked to bill the parent. When receiving a payment under the parent name, not all of the child invoices populate. I have double and triple checked that this is done correctly and can't find a reason why. Has anyone else come across this?  Do you have a solution other than receiving a partial payment to the parent account for the invoices that populate and then several other payments under the child accounts that don't populate, then create a deposit for all the separate "received payments"?