two payments left unreconciled

Have your previous months' reconciliations been correct?  When you say "ending balance" in terms of reconciliation, generally that means the bank statement ending balance, which is what you enter in the Ending Balance field in the reconciliation window.  Then if you are encounter the 8K in the Difference field, it means that you have either not enough deposits and credits posted or not enought checks and debits posted, depending on which way the difference goes (positive or negative). Just make sure you are not confusing the bank statement's ending balance with the register balance in QuickBooks, because they are not the same thing.

The register balance as of the statement ending date includes any uncleared checks, but the bank statement ending balance does not.  When you have completed a bank reconciliation it is the Cleared Balance on the reconciliation report that should match the bank statement's ending balance.

As to the duplicate paychecks, there are several things you need to take into consideration:  Were these duplicate checks included in the payroll tax reports?  If so, you will need to file corrected payroll tax reports.  Since these duplicate checks were from a closed accounting period, you should also check with your accountant, as voiding the checks or reversing them by journal entry could impact your company's income tax reports for that year.  Do you use QuickBooks Enhanced Payroll to prepare the payroll checks?

Andrea