Hi getwellwithgen,
One reason you may be seeing this is if the Paid Date has been input prior to the Invoice Date - check on the Receive Payment date and compare this to your invoice, as if this is the case it will cause the invoice to show as unpaid on eg the A/R Ageing Report. Amending the payment to be dated after the invoice (or amending the invoice to be prior to the payment) should resolve this.
If this is not the case, there are some other reasons. If the invoices are being paid with open customer credits, ensure there has still been a Receive Payment created to link the credit and the invoice together (see Option 1 on this article). It is also worth checking for any payments that may have been matched to the wrong invoice by mistake.
Please feel free to reply with some more information if you require further assistance as I'm here to help, or reach out to our Support team directly on 1800 046 038 so they can look at this in real time.
-Kass
