This could occur in two different scenarios, below are the examples :
Scenario 1 : If you have already done a transaction ( created a invoice) in your QuickBooks, which is marked as unpaid for a particular customer with the transaction amount. Now when you are trying to again post the invoice with the same transaction amount and for the same customer, Unify will not mark this as paid.
Instead Unify will "mark as paid" the first invoice which is already present.
Let us understand this case with an example.
Suppose there is a customer named as "Anjali". You have posted this customer to QuickBooks (This time the option of "Mark invoice paid" is not selected), an invoice will be created in QBs as "unpaid". Now if you try to post the same customer for the second to QBs (Having "Mark invoice paid" option selected), a new invoice will be created in QBs as "unpaid".
In the above mentioned example, instead of marking the new invoice as "paid", Unify will mark the old invoice (created at the first time) as "paid", as shown in the picture below:
Scenario 2 : If the payment status for the order is unpaid in Unify, in this case it will not "mark the invoice as paid".