A partial payment can look like a success in the bank feed and a problem in the ledger at the same time. The wire cleared, but the amount may not match the approved pay application, the schedule of values, the retainage calculation, or the change orders that were supposed to move with the draw. The unresolved difference is what ages into a dispute. Reconcile the payment at the line level. Match the QuickBooks invoice to the portal row, then compare billed, approved, withheld, and paid amounts. Look for a change order sitting on a different schedule-of-values line, a retainage percentage that changed, a back-charge, or a conditional waiver that was treated as final. A single total in the bank does not explain which work was underpaid. Keep the original pay application, portal export, waiver, and bank confirmation together. If the general contractor says the balance will be included next cycle, capture that statement and the pay-app date instead of relying on memory. Drumtap surfaces the discrepancy and the supporting evidence; you decide what to send and when. See the six sample findings and the partial-payment case study for the same pattern in a worked example.