What you may be experiencing:

The item receipt values may be incorrect in QuickBooks for items that had the discount/freight/fee selected to spread on the receiving voucher in Point of Sale.
The original Receiving Voucher in Point of Sale will have different item cost values when compared to the Item Receipt or Bill in QuickBooks once it is brought over via the financial exchange.

What you can try now:

You may edit the values in QuickBooks on the Item Receipt/Bill to reflect the correct ones from Point of Sale.

Current Status:

At this time, we are continuing to look into root cause and possible solutions. Currently, we do not have any additional information to provide.

9/27/2018