If you are participating in Amazon's Business to Business selling program you may see more settlements than you expect in A2X, these will typically be for smaller amounts than your usual settlements, and be happening on a different cycle/schedule to your usual settlements.
These parallel settlements are paid out to you from a different Amazon entity, which is why they are separate. To find them in Seller Central you can look in Reports > Payments, click on the 'Invoiced Orders' button here:
Then you should see the Amazon Pay by Invoice settlements, and be able to reconcile those to payments in your bank account exactly the same way as the main settlements.
You can find out more about how Amazon's Pay by Invoice system works and the settlement processes in Seller Central help section, or by raising a case with Amazon seller support. There's also discussions on Amazon's seller forums about it.