This could be because of the following reasons:
The Paytron user has chosen for their accountant to perform the reconciliation in Xero because they don't know which accounting code to use. In this case we will push a payment as soon as it happens, into Xero as a bank feed. The Xero user then has to manually reconcile this item.
When money is deposited into Paytron, either through a transfer from another bank account or by one of your customers, we will push that entry into your Business account as a real time bank feed. The Xero user then has to reconcile that deposit manually
Sometimes gremlins could make their way into either Xero or Paytron causing the systems to momentarily be out of sync. We actively monitor for this and when it happens we will push the missing entries into Xero as soon as we can.