How does Payables prorate the matched amount against multiple distribution lines?

We have a situation wherein an invoice was matched to a PO with 1 line, 1 shipment line with 2 distribution lines.  Receipts were applied and distributed correctly.  However when the invoice was matched, it was matched at the shipment level and the corresponding distributed amount did not match what was received.

Example:

PO Shipment line 1 quantity ordered = 65000

PO Distribution:

Line 1 quantity = 61,750;  quantity_delivered = 61,750

Line 2 quantity = 3,250;  quantity_delivered = 3,250

When invoice was matched at the shipment level, the distributed amounts automatically generated as:

Line 1 = 62,078.65  (causing an over-match of 328.65)

Line 2 = 2,921.35  (causing an under-match of 328.65)

This is causing issues with Receipt Accruals at period-end.

I know this is a training issue, but I would like to get an idea of how the items were automatically distributed (if it's following a setup formula) as I know our Payables folks will be asking the same question.