There are so many posibilities and these will vary according to how you use Quickfile.
One quick check is to see if there is a compensating error in the cheque holding account. When manually tagging an invoice that is paid by cheque it is an easy mistake to show it as paid from the current account. When you import your transactions the banking will register as a transfer from the cheque holding account leaving an outstanding balance there.
Next your best bet is to work back in your bank statements, say at each month end until you find a point where it agrees with QF and then work forward from there. Once you pin down the date where the discrepancy occurs identifying the difference should be trivial.
You really do need to verify the bank account balance as shown in QF at least once a month. At the same time ensure that unbanked cheques add up to the total in the cheque holding account.