I have recently experienced a very similar situation after recently upgrading to QB Enterprise M&W 21.0.  We had a PO that was created while using version 20.  The item was received prior to upgrading to version 21.  Now, I received the bill for the product (after the upgrade) and when I go to record the bill, only the Item Receipt shows up in the list to select from.  If I create the bill from the item receipt, it does not link the PO to the bill, leaving the line item showing as unbilled.  The Item Receipt is linked to the PO and the bill is linked to the Item Receipt, but the bill is not linked to the PO.

I rebuilt the company file and then tried deleting the bill and item receipt and re-created both with the same results. Not sure where to turn next.  Tech Support was unable to figure out the issue either.  Any suggestions?