This is happening because "Retainage is sent to an asset account" so the amount of the retainage item will never appear on your P&L until you remove it from the asset account and shift it to income (negative income.)
You can do this directly on the invoice once it is paid or on another sales transaction such as another invoice or a sales receipt.
To do this, reverse the retainage item first used on the invoice and then add an item that uses an income account. These items will cancel each other out for the invoice total.
