The leak isn't in the deal
Most resellers price individual deals carefully. The margin goes missing afterwards: a substitute line that cost more than quoted, a deal registration nobody filed, freight that never made it onto the invoice.
Every handoff is a chance to lose it
When a quote becomes a PO in another system, someone re-keys it. When the shipment becomes an invoice in a third, someone re-keys it again. Each copy is a chance for the number to drift.
Where to look first
Compare quoted cost to billed cost on your last fifty orders. Check how many deals had registration available but not filed. Look for freight and fees that were paid but never billed.
What fixes it
Keep the quote, the PO, the shipment and the invoice on one record, so the cost you quoted is the cost you buy at and the line you ship is the line you bill.
Start small
You don't need to change everything at once. Start with the handoff that leaks the most, usually quote to PO, and work outward from there.