How to Remove Milestone Hold when Invoicing Complex PO Work Confirmation

Our client has need to create Complex POs with a Goods Line Type (in R12). We recently applied a patch to allow us to create work confirmations for decimal quantities. However, because a Goods Line Type automatically defaults to a 'Milestone' Pay Item - we are receiving the following system hold on the invoice: "Invoice Quantity or Amount is not equal to the Milestone Pay Item."

Has anyone come across this issue and found a resolution or workaround? It seems strange that the patch is intended to allow decimal quantities received on a work confirmation for less than the Milestone amount, yet you cannot move forward with invoicing the confirmation. Any help would be much appreciated! Thanks.