Once a payment is received in Xero, it isn’t marked paid just yet. First, it has to be reconciled manually, and only then is it marked as a paid payment.
However, previously all payments from Xero, both reconciled and non-reconciled, have been pulled into EZRentOut after every sync. When this is done, the Order in EZRentOut is marked as paid. And because syncs in Xero are always two-way, therefore the paid Order from EZRentOut goes back to Xero and marks the non-reconciled payment as paid as well.
The solution to this problem can be found by going to Settings → Add Ons → Integrate Xero. Here, you have the option of choosing to only sync reconciled payments:
Don’t forget to click ‘Update’ once you’ve chosen the required settings.