There are several reasons why you might receive a message that not all Payment files have been processed when processing the End of Pay.
Restore to before Payment File was exported
If you restored your database to a point before exporting the Payment file. You will need to produce the file again. Verify which Payment File needs to be uploaded to your banking software and only upload the correct file.
Multiple Company Banks
If you have multiple Company Banks, an employee may be attached to the wrong Company Bank and they have been missed when you produced your Payment file. To find the mismatch, use Generate Payments:
Go to Payroll, Transactions, Import and Export, Generate Payment.
Select all for Payroll Company and Location.
Leave From Employee and To Employee blank so that all employees are included.
Select the Pay Frequency you are processing.
For Company Bank, select the first in the list.
Select the Period End Date you are processing.
Click Preview.
If you receive a message that there are no records. Select the next Company Bank in the list and click Preview.
You will find the mismatch because the Preview will produce a report.
Close the Preview.
You can then either produce the Payment file or correct the employee record:
To produce the file:
Check that the remaining parameters are correct.
Click File to produce the Payment file for the combination. This will mark the pays as being generated. The file can be either:
uploaded to the bank.
discarded and you pay the employee manually through your banking software.
To correct the employee record:
Delete the transaction (Payroll, Transactions, Processing, Extended Timesheet).
Correct the bank details for the employee (Payroll, Maintenance, Employees, Employees).
Re-key the pay.
Then produce a second bank file to be uploaded to the bank, containing just the one employee.