I am reconciling my credit card statements, but the credit card payments made from my checking account are not showing up under reconcile. This is causing the reconcile to be off by the exact payment amount. When I go into the register, the payment does show there as having been credited to the credit card, but it shows as already reconciled. I guess it was reconciled on the checking account side. When I try to unreconcile and go back to reconcile to check it off then the balance is off by that amount. How do I rectify this?

The credit card payment was downloaded from the checking account and reconciled there. Did I miss a step somewhere?