Have the same problem.
Hi Sadie
Can you please follow the steps in my previous reply and let me know how you go:
Go to Accounting>>Manage linked categories>Payroll tab and make sure the Bank account for xxxx payments is the correct account.
Go to Banking>>Find transactions>>locate and open one of those pay transactions and check the Account field is the correct bank account.
If the pay transactions have been posted to the correct bank account, go to Banking>>Reconcile accounts and check if those pays are ticked. If they are, untick them and they will appear to be matched in Bank transactions.
You'll also need to check the Payment method selected in employee card>>Payment details. If it's electronic and the pay transactions have been posted to the electronic clearing account following the instructions in this post: Why can't I match employee pays in Bank transactions
